df3io.cpp

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/*
 * Author: Grant Tang, 08/06/2010 (gtang@bcm.edu)
 * Copyright (c) 2000-2010 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 <algorithm>
#include <climits>
 
#include "df3io.h"
#include "portable_fileio.h"
 
using namespace EMAN;
 
Df3IO::Df3IO(const string & fname, IOMode rw)
:       ImageIO(fname, rw),
        is_new_file(false), rendermin(0.0), rendermax(0.0), renderbits(16)
{
}
 
Df3IO::~Df3IO()
{
        if (file) {
                fclose(file);
                file = 0;
        }
}
 
void Df3IO::init()
{
        ENTERFUNC;
        if (initialized) {
                return;
        }
 
        initialized = true;
        file = sfopen(filename, rw_mode, &is_new_file);
 
        EXITFUNC;
}
 
// header is 3 MSB unsigned shorts (nx,ny,nz) in big-endian
int Df3IO::read_header(Dict & dict, int, const Region *, bool )
{
        ENTERFUNC;
        init();
        size_t nr;
 
        if (!is_new_file) {
                if (fread(&nx, sizeof(unsigned short), 1, file) != 1) {
                        throw ImageReadException(filename, "DF3 header");
                }
 
                nr = fread(&ny, sizeof(unsigned short), 1, file); nr++;
                nr = fread(&nz, sizeof(unsigned short), 1, file); nr++;
 
                if(!ByteOrder::is_host_big_endian()) {
                        ByteOrder::swap_bytes(&nx);
                        ByteOrder::swap_bytes(&ny);
                        ByteOrder::swap_bytes(&nz);
                }
 
                dict["nx"] = (int)nx;
                dict["ny"] = (int)ny;
                dict["nz"] = (int)nz;
        }
 
        EXITFUNC;
        return 0;
}
 
int Df3IO::write_header(const Dict & dict, int, const Region*, EMUtil::EMDataType, bool)
{
        ENTERFUNC;
        init();
 
        nx = (unsigned short)((int)dict["nx"]);
        ny = (unsigned short)((int)dict["ny"]);
        nz = (unsigned short)((int)dict["nz"]);
 
        portable_fseek(file, 0, SEEK_SET);
 
        unsigned short df3header[3];
        df3header[0] = nx;
        df3header[1] = ny;
        df3header[2] = nz;
        ByteOrder::become_big_endian(df3header, 3);
 
        EMUtil::getRenderLimits(dict, rendermin, rendermax, renderbits);
 
        if(fwrite(df3header, sizeof(unsigned short), 3, file) != 3) {
                throw ImageWriteException(filename, "DF3 header");
        }
 
        EXITFUNC;
        return 0;
}
 
int Df3IO::read_data(float *rdata, int, const Region *, bool)
{
        ENTERFUNC;
 
        size_t image_size = (size_t)nx*ny*nz;
        size_t nr;
 
        // obtain file size:
        portable_fseek (file , 0 , SEEK_END);
        size_t fsize = ftell (file);
        rewind (file);
 
        unsigned int * uidata = 0;
        unsigned short * usdata = 0;
        unsigned char * ucdata = 0;
 
        portable_fseek(file, sizeof(unsigned short)*3, SEEK_SET);       //skip header
        switch(fsize/image_size) {
        case sizeof(unsigned int):
                uidata = new unsigned int[image_size];
                nr = fread(uidata, sizeof(unsigned int), image_size, file); nr++;
                become_host_endian < unsigned int >(uidata, image_size);
                std::copy(uidata, uidata+image_size, rdata);
                if(uidata) {delete [] uidata; uidata=0;}
                break;
        case sizeof(unsigned short):
                usdata = new unsigned short[image_size];
                nr = fread(usdata, sizeof(unsigned short), image_size, file); nr++;
                become_host_endian < unsigned short >(usdata, image_size);
                std::copy(usdata, usdata+image_size, rdata);
                if(usdata) {delete [] usdata; usdata=0;}
                break;
        case sizeof(unsigned char):
                ucdata = new unsigned char[image_size];
                nr = fread(ucdata, sizeof(unsigned char), image_size, file); nr++;
                std::copy(ucdata, ucdata+image_size, rdata);
                if(ucdata) {delete [] ucdata; ucdata=0;}
                break;
        default:
                throw ImageReadException(filename, "DF3 does not support this kind of data type.");
        }
 
        EXITFUNC;
        return 0;
}
 
int Df3IO::write_data(float *data, int, const Region*,
                                          EMUtil::EMDataType dt, bool)
{
        ENTERFUNC;
 
        size_t img_size = (size_t)nx*ny*nz;
        unsigned int * uidata = 0;
        unsigned short * usdata = 0;
        unsigned char * ucdata = 0;
 
        int truebits=EMDataTypeBits[(int)dt];
        if (renderbits==0 || renderbits>truebits) renderbits=truebits;
        EMUtil::getRenderMinMax(data, nx, ny, rendermin, rendermax, renderbits,  nz);
 
        switch(dt) {
        case EMUtil::EM_UINT:
                uidata = new unsigned int[img_size];
                for (size_t i = 0; i < img_size; ++i) {
                        if(data[i] <= rendermin) {
                                uidata[i] = 0;
                        }
                        else if(data[i] >= rendermax) {
                                uidata[i] = UINT_MAX;
                        }
                        else {
                                uidata[i]=(unsigned int)((data[i]-rendermin)/(rendermax-rendermin)*UINT_MAX);
                        }
                }
                ByteOrder::become_big_endian(uidata, img_size);
                if(fwrite(uidata, sizeof(unsigned int), img_size, file) != img_size) {
                        throw ImageWriteException(filename, "DF3 unsigned int data");
                }
                if(uidata) {delete [] uidata; uidata=0;}
                break;
        case EMUtil::EM_USHORT:
                usdata = new unsigned short[img_size];
                for (size_t i = 0; i < img_size; ++i) {
                        if(data[i] <= rendermin) {
                                usdata[i] = 0;
                        }
                        else if(data[i] >= rendermax) {
                                usdata[i] = USHRT_MAX;
                        }
                        else {
                                usdata[i]=(unsigned short)((data[i]-rendermin)/(rendermax-rendermin)*USHRT_MAX);
                        }
                }
                ByteOrder::become_big_endian(usdata, img_size);
                if(fwrite(usdata, sizeof(unsigned short), img_size, file) != img_size) {
                        throw ImageWriteException(filename, "DF3 unsigned short data");
                }
                if(usdata) {delete [] usdata; usdata=0;}
                break;
        case EMUtil::EM_UCHAR:
                ucdata = new unsigned char[img_size];
                for (size_t i = 0; i < img_size; ++i) {
                        if(data[i] <= rendermin) {
                                ucdata[i] = 0;
                        }
                        else if(data[i] >= rendermax){
                                ucdata[i] = UCHAR_MAX;
                        }
                        else {
                                ucdata[i]=(unsigned char)((data[i]-rendermin)/(rendermax-rendermin)*UCHAR_MAX);
                        }
                }
                if(fwrite(ucdata, sizeof(unsigned char), img_size, file) != img_size) {
                        throw ImageWriteException(filename, "DF3 unsigned char data");
                }
                if(ucdata) {delete [] ucdata; ucdata=0;}
                break;
        default:
                throw ImageWriteException(filename,"DF3 does not support this data format");
        }
 
        EXITFUNC;
        return 0;
}
 
void Df3IO::flush()
{
        fflush(file);
}
 
bool Df3IO::is_image_big_endian()
{
        return true;    //DF3 file is always big endian
}
 
bool Df3IO::is_complex_mode()
{
        return false;   //DF3 only support real image
}
 
bool Df3IO::is_valid(const void *first_block, off_t)
{
        ENTERFUNC;
 
        if (!first_block) {
                return false;
        }
 
        const unsigned short *data = static_cast < const unsigned short *>(first_block);
        unsigned short nx = data[0];
        unsigned short ny = data[1];
        unsigned short nz = data[2];
 
        if(ByteOrder::is_data_big_endian(&nx) && ByteOrder::is_data_big_endian(&ny) && ByteOrder::is_data_big_endian(&nz)) {
                return true;
        }
 
        EXITFUNC;
        return false;
}