fitsio.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 "fitsio.h"
#include "portable_fileio.h"
#include "geometry.h"
#include "util.h"
#include "ctf.h"
 
using namespace EMAN;
 
FitsIO::FitsIO(const string & fname, IOMode rw)
:       ImageIO(fname, rw)
{
        is_big_endian = ByteOrder::is_host_big_endian();
        is_new_file = false;
}
 
FitsIO::~FitsIO()
{
        if (file) {
                fclose(file);
                file = 0;
        }
}
 
void FitsIO::init()
{
        ENTERFUNC;
 
        if (initialized) {
                return;
        }
 
        initialized = true;
        file = sfopen(filename, rw_mode, &is_new_file);
 
        EXITFUNC;
}
 
 
bool FitsIO::is_image_big_endian()
{
        init();
        return is_big_endian;
}
 
bool FitsIO::is_valid(const void *first_block, off_t)
{
        ENTERFUNC;
 
        if (!first_block) {
                return false;
        }
 
        if (strncmp("SIMPLE  ",(const char *)first_block,8)==0) return true;
 
        EXITFUNC;
        return false;
}
 
int FitsIO::read_header(Dict & dict, int image_index, const Region * area, bool )
{
        ENTERFUNC;
 
//      dict["apix_x"] = mrch.xlen / (mrch.nx - 1);
//      dict["apix_y"] = mrch.ylen / (mrch.ny - 1);
        //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 (area) throw ImageReadException(filename,"Area reading not supported for FITS format");
 
        dict["nx"]=1;
        dict["ny"]=1;
        dict["nz"]=1;
 
        char s[81],lbl[9],val[80];
//      int dim=0;
        s[80]=0;
        rewind(file);
        size_t nr;
        for (nr = fread(s,80,1,file); strncmp("END",s,3); nr = fread(s,80,1,file)) {
                nr = nr;
                sscanf(s,"%8s = %[^/]",lbl,val);
//              printf("%s,%s\n",lbl,val);
                if (strncmp("SIMPLE  ",s,8)==0) continue;
                else if (strncmp("END     ",s,8)==0) break;
//              else if (strncmp("BITPIX  ",s,8)==0)
//              else if (strncmp("NAXIS   ",s,8)==0) dim=atoi(val);
                else if (strncmp("NAXIS",s,5)==0) {
                        if (s[5]=='1') dict["nx"]=atoi(val);
                        if (s[5]=='2') dict["ny"]=atoi(val);
                        if (s[5]=='3') dict["nz"]=atoi(val);
                }
                else {
                        dict[(string)"FITS."+lbl]=val;
                }
        }
 
        dstart=((ftell(file)-1)/2880+1)*2880;
 
        int xlen = 0, ylen = 0, zlen = 0;
        dtype=atoi(dict["FITS.BITPIX"]);
        EMUtil::get_region_dims(area, dict["nx"], &xlen, dict["ny"], &ylen, dict["nz"], &zlen);
 
        dict["nx"] = nx=xlen;
        dict["ny"] = ny=ylen;
        dict["nz"] = nz=zlen;
 
        EXITFUNC;
        return 0;
}
 
int FitsIO::write_header(const Dict &, int, const Region*, EMUtil::EMDataType, bool)
{
        ENTERFUNC;
//      check_write_access(rw_mode, image_index, 1);
        LOGWARN("FITS write is not supported.");
        EXITFUNC;
        return 0;
}
 
int FitsIO::read_data(float *rdata, int image_index, const Region *, bool )
{
        ENTERFUNC;
        size_t i;
        size_t nr;
        size_t size = (size_t)nx*ny*nz;
 
        //single image format, index can only be zero
        image_index = 0;
        check_read_access(image_index, rdata);
 
        portable_fseek(file, dstart, SEEK_SET);
        unsigned char *cdata=(unsigned char *)rdata;
        short *sdata=(short *)rdata;
        int *idata=(int *)rdata;
        double *ddata;
 
        switch (dtype) {
        case 8:
                nr = fread(cdata,nx,ny*nz,file); nr++;
                for (i=size-1; i<size; i--) rdata[i]=cdata[i];
                break;
        case 16:
                nr = fread(cdata,nx,ny*nz*2,file); nr++;
                if (!ByteOrder::is_host_big_endian()) ByteOrder::swap_bytes((short*) sdata, size);
                for (i=size-1; i<size; i--) rdata[i]=sdata[i];
                break;
        case 32:
                nr = fread(cdata,nx,ny*nz*4,file); nr++;
                if (!ByteOrder::is_host_big_endian()) ByteOrder::swap_bytes((int*) rdata, size);
                for (i=0; i<size; i++) rdata[i]=static_cast<float>(idata[i]);
                break;
        case -32:
                nr = fread(cdata,nx*4,ny*nz,file); nr++;
                if (!ByteOrder::is_host_big_endian()) ByteOrder::swap_bytes((float*) rdata, size);
                break;
        case -64:
                ddata=(double *)malloc(size*8);
                nr = fread(ddata,nx,ny*nz*8,file); nr++;
                if (!ByteOrder::is_host_big_endian()) ByteOrder::swap_bytes((double*) ddata, size);
                for (i=0; i<size; i++) rdata[i]=static_cast<float>(ddata[i]);
                free(ddata);
                break;
        }
 
        EXITFUNC;
        return 0;
}
 
int FitsIO::write_data(float *data, int image_index, const Region*,
                                          EMUtil::EMDataType, bool)
{
        ENTERFUNC;
 
        check_write_access(rw_mode, image_index, 1, data);
//      check_region(area, FloatSize(mrch.nx, mrch.ny, mrch.nz), is_new_file);
 
 
        EXITFUNC;
        return 0;
}
 
 
bool FitsIO::is_complex_mode()
{
        init();
        return false;
}
 
void FitsIO::flush()
{
        fflush(file);
}
 
int FitsIO::read_ctf(Ctf &, int)
{
        ENTERFUNC;
        init();
        EXITFUNC;
        return 0;
}
 
void FitsIO::write_ctf(const Ctf &, int)
{
        ENTERFUNC;
        init();
 
        EXITFUNC;
}