imagicio.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 "imagicio.h"
#include "portable_fileio.h"
#include "util.h"
#include "geometry.h"
#include "ctf.h"
#include "emassert.h"
#include "transform.h"
 
#include <ctime>
 
using namespace EMAN;
 
const char *ImagicIO::HED_EXT = "hed";
const char *ImagicIO::IMG_EXT = "img";
const char *ImagicIO::REAL_TYPE_MAGIC = "REAL";
const char *ImagicIO::CTF_MAGIC = "!-";
 
ImagicIO::ImagicIO(const string & fname, IOMode rw)
:       ImageIO(fname, rw), hed_file(0), img_file(0)
{
        hed_filename = Util::change_filename_ext(filename, HED_EXT);
        img_filename = Util::change_filename_ext(filename, IMG_EXT);
 
        is_big_endian = ByteOrder::is_host_big_endian();
        is_new_hed = false;
        is_new_img = false;
        memset(&imagich, 0, sizeof(ImagicHeader));
        imagich.count = -1;
        datatype = IMAGIC_UNKNOWN_TYPE;
        nz = 0;
}
 
ImagicIO::~ImagicIO()
{
        if (hed_file) {
                fclose(hed_file);
                hed_file = 0;
        }
 
        if (img_file) {
                fclose(img_file);
                img_file = 0;
        }
}
 
void ImagicIO::init()
{
        ENTERFUNC;
 
        if (initialized) {
                return;
        }
 
        initialized = true;
 
        is_new_hed = false;
        is_new_img = false;
 
        hed_file = sfopen(hed_filename, rw_mode, &is_new_hed);
        img_file = sfopen(img_filename, rw_mode, &is_new_img);
 
        if (is_new_hed != is_new_img) {
                LOGWARN("IMAGIC header file and data file should both exist or both not exist");
        }
 
        if (!is_new_hed) {
                if (fread(&imagich, sizeof(ImagicHeader), 1, hed_file) != 1) {
                        throw ImageReadException(hed_filename, "IMAGIC header");
                }
 
//              if (!is_valid(&imagich)) {
//                      throw ImageReadException(hed_filename, "invalid IMAGIC file");
//              }
 
                datatype = get_datatype_from_name(imagich.type);
 
                if (datatype != IMAGIC_USHORT && datatype != IMAGIC_FLOAT) {
                        LOGERR("unsupported imagic data type: %s", imagich.type);
                        throw ImageReadException(hed_filename, "unsupported imagic data type");
                }
 
                is_big_endian = ByteOrder::is_data_big_endian(&imagich.ny);
                make_header_host_endian(imagich);
                rewind(hed_file);
        }
        EXITFUNC;
}
 
bool ImagicIO::is_valid(const void *first_block)
{
        ENTERFUNC;
 
        if (!first_block) {
                return false;
        }
 
        const int *data = static_cast < const int *>(first_block);
        int count = data[1];
        int headrec = data[3];
        int month = data[5];
        int hour = data[7];
        int nx = data[13];
        int ny = data[12];
        
        bool data_big_endian = ByteOrder::is_data_big_endian(&headrec);
 
        if (data_big_endian != ByteOrder::is_host_big_endian()) {
                ByteOrder::swap_bytes(&count);
                ByteOrder::swap_bytes(&headrec);
                ByteOrder::swap_bytes(&month);
                ByteOrder::swap_bytes(&hour);
                ByteOrder::swap_bytes(&nx);
                ByteOrder::swap_bytes(&ny);
        }
 
        const int max_dim = 1 << 20;
        bool result = false;
 
        if (headrec == 1 &&
                count >= 0 && count < max_dim &&
                nx > 0 && nx < max_dim &&
                ny > 0 && ny < max_dim && month >= 0 && hour >= 0 && hour <= 24) {
                result = true;
        }
 
        EXITFUNC;
        return result;
}
 
int ImagicIO::read_header(Dict & dict, int image_index, const Region * area, bool is_3d)
{
        ENTERFUNC;
 
        check_read_access(image_index);
 
        int nimg = 1;
 
        if (is_3d) {
                nimg = imagich.count + 1;
 
                if (nimg <= 1) {
                        LOGWARN("this is not a 3D IMAGIC. Read as a 2D");
                }
        }
 
        ImagicHeader hed;
        if (image_index == 0) {
                hed = imagich;
        }
        else {
                memset(&hed, 0, sizeof(ImagicHeader));
                portable_fseek(hed_file, sizeof(ImagicHeader) * image_index, SEEK_SET);
                fread(&hed, sizeof(ImagicHeader), 1, hed_file);
                make_header_host_endian(hed);
        }
        check_region(area, FloatSize(hed.nx, hed.ny, nimg), is_new_hed,false);
 
    datatype = get_datatype_from_name(imagich.type);
 
        int xlen = 0, ylen = 0, zlen = 0;
        EMUtil::get_region_dims(area, hed.nx, &xlen, hed.ny, &ylen, nimg, &zlen);
 
        dict["nx"] = xlen;
        dict["ny"] = ylen;
        dict["nz"] = zlen;
 
        dict["datatype"] = to_em_datatype(datatype);
 
        dict["minimum"] = hed.min;
        dict["maximum"] = hed.max;
        dict["mean"] = hed.avdens;
        dict["sigma"] = hed.sigma;
 
        dict["IMAGIC.imgnum"] = hed.imgnum;
        dict["IMAGIC.count"] = hed.count;
        dict["IMAGIC.error"] = hed.error;
 
        dict["IMAGIC.headrec"] = hed.headrec;
        dict["IMAGIC.mday"] = hed.mday;
        dict["IMAGIC.month"] = hed.month;
 
        dict["IMAGIC.year"] = hed.year;
        dict["IMAGIC.hour"] = hed.hour;
        dict["IMAGIC.minute"] = hed.minute;
 
        dict["IMAGIC.sec"] = hed.sec;
        dict["IMAGIC.reals"] = hed.reals;
        dict["IMAGIC.pixels"] = hed.pixels;
 
        char tmp[5] = { hed.type[0],hed.type[1],hed.type[2],hed.type[3],0 };
        dict["IMAGIC.type"] = tmp;
        dict["IMAGIC.ixold"] = hed.ixold;
        dict["IMAGIC.iyold"] = hed.iyold;
 
        dict["IMAGIC.oldav"] = hed.oldav;
        dict["IMAGIC.label"] = hed.label;
        dict["ptcl_repr"] = hed.mrc2;                   // raw images represented by this image
 
        dict["orientation_convention"] = "EMAN";
    const float alt = hed.mrc1[1]*180.0f/M_PI;
    const float az = hed.mrc1[2]*180.0f/M_PI;
    const float phi = hed.mrc1[0]*180.0f/M_PI;
        dict["euler_alt"] = alt;
        dict["euler_az"] = az;
        dict["euler_phi"] = phi;
        Transform *trans = new Transform();
        trans->set_rotation(Dict("type", "eman", "alt", alt, "az", az, "phi", phi));
        if( hed.count==0 ) {
                dict["xform.projection"] = trans;
        }
        else {
                dict["xform.projection"] = trans;
                dict["xform.align3d"] = trans;
        }
        Ctf * ctf_ = read_ctf(hed);
        if( ctf_ != 0) {
                dict["ctf"] = ctf_;
        }
        if(trans) {delete trans; trans=0;}
        if(ctf_) {delete ctf_; ctf_=0;}
        EXITFUNC;
        return 0;
}
 
int ImagicIO::write_header(const Dict & dict, int image_index,
                                                   const Region * area, EMUtil::EMDataType, bool use_host_endian)
{
        ENTERFUNC;
 
        if(image_index<0) {
                image_index = get_nimg();
        }
 
        check_write_access(rw_mode, image_index);
        nz = dict["nz"];
        if (nz > 1 && image_index != 0) {
                throw ImageWriteException(filename, "to write 3D IMAGIC image, image index must be 0");
        }
 
        if (area) {
                check_region(area, FloatSize(imagich.nx, imagich.ny, imagich.count+1),
                                         is_new_hed);
                EXITFUNC;
                return 0;
        }
 
        int nx = dict["nx"];
        int ny = dict["ny"];
        int nimg=0;             //# images currently in file
 
 
        if (!is_new_hed) {
        datatype = get_datatype_from_name(imagich.type);
 
                if (imagich.nx != nx || imagich.ny != ny) {
                        char desc[256];
                        sprintf(desc, "new IMAGIC size %dx%d is not equal to existing size %dx%d",
                                        nx, ny, imagich.nx, imagich.ny);
                        throw ImageWriteException(filename, desc);
                }
 
        if (datatype!=IMAGIC_FLOAT) {
                        throw ImageWriteException(filename, "Attempted write to non REAL Imagic file");
                }
 
        rewind(hed_file);
                nimg=imagich.count+1;
        }
 
        ImagicHeader new_hed;
        memset(&new_hed, 0, sizeof(ImagicHeader));
 
        time_t cur_time = time(0);
        struct tm *tm = localtime(&cur_time);
 
        new_hed.error = 0;
        new_hed.headrec = 1;
 
        new_hed.mday = tm->tm_mday;
        new_hed.month = tm->tm_mon;
        new_hed.year = tm->tm_year + 1900;
        new_hed.hour = tm->tm_hour;
        new_hed.minute = tm->tm_min;
        new_hed.sec = tm->tm_sec;
 
        new_hed.reals = nx * ny;
        new_hed.pixels = nx * ny;
        new_hed.ny = ny;
        new_hed.nx = nx;
 
        new_hed.ixold = 0;
        new_hed.iyold = 0;
        new_hed.oldav = 0;
 
        new_hed.min = (float)dict["minimum"];
        new_hed.max = (float)dict["maximum"];
        new_hed.avdens = (float)dict["mean"];
        new_hed.sigma = (float)dict["sigma"];
 
        if(nz<=1 && dict.has_key("xform.projection")) {
                Transform * t = dict["xform.projection"];
                Dict d = t->get_rotation("eman");
                new_hed.mrc1[1] = (float)d["alt"]*M_PI/180.0f;
                new_hed.mrc1[2] = (float)d["az"]*M_PI/180.0f;
                new_hed.mrc1[0] = (float)d["phi"]*M_PI/180.0f;
                if(t) {delete t; t=0;}
        }
        else if(nz>1 && dict.has_key("xform.align3d")) {
                Transform * t = dict["xform.align3d"];
                Dict d = t->get_rotation("eman");
                new_hed.mrc1[1] = (float)d["alt"]*M_PI/180.0f;
                new_hed.mrc1[2] = (float)d["az"]*M_PI/180.0f;
                new_hed.mrc1[0] = (float)d["phi"]*M_PI/180.0f;
                if(t) {delete t; t=0;}
        }
        else {
                if(dict.has_key("euler_alt")) new_hed.mrc1[1] = (float)dict["euler_alt"]*M_PI/180.0f;
                if(dict.has_key("euler_az")) new_hed.mrc1[2] = (float)dict["euler_az"]*M_PI/180.0f;
                if(dict.has_key("euler_phi")) new_hed.mrc1[0] = (float)dict["euler_phi"]*M_PI/180.0f;
        }
 
        if(dict.has_key("ptcl_repr")) new_hed.mrc2 = (int)dict["ptcl_repr"];
 
        string new_label = dict.has_key("IMAGIC.label") ? (string) dict["IMAGIC.label"] : "";
        sprintf(new_hed.label, "%s", new_label.c_str() );
 
        new_hed.lbuf = nx;
        new_hed.inn = 1;
        new_hed.iblp = ny;
        new_hed.ifb = 0;
        new_hed.lbw = 0;
        new_hed.lbr = -1;
        new_hed.lastlr = -1;
        new_hed.lastlw = 1;
        new_hed.num = 8;
        new_hed.nhalf = nx / 2;
        new_hed.ibsd = nx * 2;
        new_hed.ihfl = 7;
        new_hed.lcbr = -1;
        new_hed.lcbw = 1;
        new_hed.imstr = -1;
        new_hed.imstw = -1;
        new_hed.istart = 1;
        new_hed.iend = nx;
        new_hed.leff = nx;
        new_hed.linbuf = nx * 2;
        new_hed.ntotbuf = -1;
        new_hed.icstart = 1;
        new_hed.icend = nx / 2;
        strncpy(new_hed.type, REAL_TYPE_MAGIC,4);
 
 
        // header in file order
        if ( (is_big_endian != ByteOrder::is_host_big_endian()) || !use_host_endian)  swap_header(new_hed);
 
        // overwrite existing header if necessary
        if (image_index>=0 && image_index<nimg) {
                portable_fseek(hed_file, sizeof(ImagicHeader)*image_index, SEEK_SET);
                new_hed.imgnum=image_index+1;
                if (is_big_endian != ByteOrder::is_host_big_endian())
                                ByteOrder::swap_bytes((int *) &new_hed.imgnum,1);
                fwrite(&new_hed, sizeof(ImagicHeader),1,hed_file);
        }
 
        // How many images does the file need when we're done ?
        int required_len;
        if (nz>1) required_len=nz;
        else {
                if (image_index<0) required_len=nimg+1;
                else if (image_index+1>nimg) required_len=image_index+1;
                else required_len=nimg;
        }
 
        // Extend the file to the necessary length
        portable_fseek(hed_file, 0, SEEK_END);
        while (nimg<required_len) {
                nimg++;
                new_hed.imgnum=nimg;
                if (is_big_endian != ByteOrder::is_host_big_endian())
                                ByteOrder::swap_bytes((int *) &new_hed.imgnum,1);
                fwrite(&new_hed, sizeof(ImagicHeader),1,hed_file);
        }
 
        // update the 1st header with total # images
        portable_fseek(hed_file, sizeof(int), SEEK_SET);
        nimg--;
        if (is_big_endian != ByteOrder::is_host_big_endian())
                        ByteOrder::swap_bytes((int *) &nimg,1);
        fwrite(&nimg, sizeof(int), 1, hed_file);
 
        // header in machine order
        if ( (is_big_endian != ByteOrder::is_host_big_endian()) || !use_host_endian)  swap_header(new_hed);
        imagich=new_hed;
        imagich.count=nimg;
        is_new_hed = false;
 
        if( dict.has_key("ctf") ) {
                Ctf * ctf_ = dict["ctf"];
                write_ctf(ctf_);
                if(ctf_) {delete ctf_; ctf_=0;}
        }
 
        EXITFUNC;
        return 0;
}
 
int ImagicIO::read_data(float *data, int image_index, const Region * area, bool is_3d)
{
        ENTERFUNC;
 
        check_read_access(image_index, data);
    Assert(datatype != IMAGIC_UNKNOWN_TYPE);
        int nimg = 1;
        if (is_3d) {
                nimg = imagich.count + 1;
        }
 
        if (is_3d && imagich.count < 1) {
                LOGWARN("this is not a 3D IMAGIC. Read as a 2D");
                is_3d = false;
        }
 
        check_region(area, FloatSize(imagich.nx, imagich.ny, nimg), is_new_hed,false);
 
        rewind(img_file);
 
        unsigned short *sdata = (unsigned short *) data;
        unsigned char *cdata = (unsigned char *) data;
        size_t mode_size = get_datatype_size(datatype);
        EMUtil::process_region_io(cdata, img_file, READ_ONLY, image_index, mode_size,
                                                          imagich.nx, imagich.ny, nimg, area, true);
 
#if 0
        int row_size = imagich.nx * mode_size;
        int sec_size = imagich.nx * imagich.ny * mode_size;
 
        for (int k = 0; k < nimg; k++) {
                for (int i = imagich.ny - 1; i >= 0; i--) {
                        if (fread(&cdata[k * sec_size + i * row_size], row_size, 1, img_file) != 1) {
                                LOGERR("incomplete data read: %d/%d blocks on file '%s'",
                                                                         i, imagich.ny, filename.c_str());
                                return 1;
                        }
                }
        }
#endif
 
        size_t img_size = imagich.nx * imagich.ny * nimg;
 
        if (datatype == IMAGIC_FLOAT) {
                become_host_endian(data, img_size);
        }
        else if (datatype == IMAGIC_USHORT) {
                become_host_endian((unsigned short *) cdata, img_size);
 
                for (int j = img_size - 1; j >= 0; j--) {
                        data[j] = static_cast < float >(sdata[j]);
                }
        }
        else {
                throw ImageReadException(filename, "unknown imagic data type");
        }
 
        EXITFUNC;
        return 0;
}
 
int ImagicIO::write_data(float *data, int image_index, const Region* area,
                                                 EMUtil::EMDataType, bool use_host_endian)
{
        ENTERFUNC;
 
        check_write_access(rw_mode, image_index, 0, data);
        check_region(area, FloatSize(imagich.nx, imagich.ny, imagich.count+1),
                                 is_new_hed);
 
        if (nz == 1) {
                if (image_index == -1) {
                        portable_fseek(img_file, 0, SEEK_END);
                }
                else {
                        size_t sec_size = imagich.nx * imagich.ny * sizeof(float);
                        portable_fseek(img_file, ((off_t) sec_size) * image_index, SEEK_SET);
                }
        }
 
        if(is_new_img) {
                if(!use_host_endian) {
                        ByteOrder::swap_bytes(data, imagich.nx * imagich.ny * nz);
                }
        }
        else if (is_big_endian != ByteOrder::is_host_big_endian()) {
                ByteOrder::swap_bytes(data, imagich.nx * imagich.ny * nz);
        }
#if 0
        int n_pad_imgs = 0;
        int old_num_imgs = imagich.count + 1;
        if (image_index > old_num_imgs) {
                n_pad_imgs = image_index - old_num_imgs;
        }
#endif
 
        // New way to write data which includes region writing.
        // If it is tested to be OK, remove the old code in the
        // #if 0  ... #endif block.
        EMUtil::process_region_io(data, img_file, WRITE_ONLY, 0,
                                                          sizeof(float), imagich.nx, imagich.ny,
                                                          nz, area, true);
 
 
#if 0
        size_t row_size = imagich.nx * sizeof(float);
        int nxy = imagich.nx * imagich.ny;
 
        for (int i = 0; i < nz; i++) {
                for (int j = imagich.ny - 1; j >= 0; j--) {
                        fwrite(&data[i * nxy + j * imagich.nx], row_size, 1, img_file);
                }
 
                if (!is_new_img && (is_big_endian != ByteOrder::is_host_big_endian())) {
                        ByteOrder::swap_bytes(data, imagich.nx * imagich.ny);
                }
        }
#endif
        EXITFUNC;
        return 0;
}
 
void ImagicIO::flush()
{
        fflush(img_file);
        fflush(hed_file);
}
 
Ctf * ImagicIO::read_ctf(const ImagicHeader& hed) const
{
        ENTERFUNC;
 
        Ctf * ctf_ = 0;
        size_t n = strlen(CTF_MAGIC);
 
        if (strncmp(imagich.label, CTF_MAGIC, n) == 0) {
                ctf_ = new EMAN1Ctf();
                string header_label(hed.label);
                // Note: this block was making things crash because it assumed the following if statement
                // was true - I added the if statement (d.woolford)
                if (header_label.size() > 2) {
                        string sctf = "O" + header_label.substr(2);
                        ctf_->from_string(sctf);
                }
        }
 
        EXITFUNC;
        return ctf_;
}
 
void ImagicIO::write_ctf(const Ctf * const ctf, int)
{
        ENTERFUNC;
        init();
 
        size_t n = strlen(CTF_MAGIC);
        strcpy(imagich.label, CTF_MAGIC);
        string ctf_ = ctf->to_string().substr(1);
        strncpy(&imagich.label[n], ctf_.c_str(), sizeof(imagich.label) - n);
 
        rewind(hed_file);
        if (fwrite(&imagich, sizeof(ImagicHeader), 1, hed_file) != 1) {
                throw ImageWriteException(hed_filename, "Imagic Header");
        }
 
        EXITFUNC;
}
 
bool ImagicIO::is_complex_mode()
{
        init();
        if (datatype == IMAGIC_FLOAT_COMPLEX || datatype == IMAGIC_FFT_FLOAT_COMPLEX) {
                return true;
        }
        return false;
}
 
bool ImagicIO::is_image_big_endian()
{
        init();
        return is_big_endian;
}
 
int ImagicIO::get_nimg()
{
        init();
        return (imagich.count + 1);
}
 
ImagicIO::DataType ImagicIO::get_datatype_from_name(const char *name)
{
        DataType t = IMAGIC_UNKNOWN_TYPE;
 
        if (strncmp(name, "PACK",4) == 0) {
                t = IMAGIC_UCHAR;
        }
        else if (strncmp(name, "INTG",4) == 0) {
                t = IMAGIC_USHORT;
        }
        else if (strncmp(name, REAL_TYPE_MAGIC,4) == 0) {
                t = IMAGIC_FLOAT;
        }
        else if (strncmp(name, "COMP",4) == 0) {
                t = IMAGIC_FLOAT_COMPLEX;
        }
        else if (strncmp(name, "RECO",4) == 0) {
                t = IMAGIC_FFT_FLOAT_COMPLEX;
        }
        return t;
}
 
size_t ImagicIO::get_datatype_size(DataType t)
{
        size_t s = 0;
        switch (t) {
        case IMAGIC_UCHAR:
                s = sizeof(unsigned char);
                break;
        case IMAGIC_USHORT:
                s = sizeof(unsigned short);
                break;
        case IMAGIC_FLOAT:
        case IMAGIC_FLOAT_COMPLEX:
        case IMAGIC_FFT_FLOAT_COMPLEX:
                s = sizeof(float);
                break;
        default:
                s = 0;
        }
 
        return s;
}
 
int ImagicIO::to_em_datatype(DataType t)
{
        switch (t) {
        case IMAGIC_UCHAR:
                return EMUtil::EM_UCHAR;
        case IMAGIC_USHORT:
                return EMUtil::EM_USHORT;
        case IMAGIC_FLOAT:
                return EMUtil::EM_FLOAT;
        case IMAGIC_FLOAT_COMPLEX:
                return EMUtil::EM_FLOAT_COMPLEX;
        default:
                break;
        }
 
        return EMUtil::EM_UNKNOWN;
}
 
void ImagicIO::make_header_host_endian(ImagicHeader & hed)
{
        if (is_big_endian != ByteOrder::is_host_big_endian()) {
                swap_header(hed);
        }
}
 
 
void ImagicIO::swap_header(ImagicHeader & hed)
{
        ByteOrder::swap_bytes((int *) &hed, NUM_4BYTES_PRE_IXOLD);
        ByteOrder::swap_bytes(&hed.ixold, NUM_4BYTES_AFTER_IXOLD);
        ByteOrder::swap_bytes((int *) &hed.space, NUM_4BYTES_AFTER_SPACE);
}