spiderio.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 "spiderio.h"
#include "geometry.h"
#include "portable_fileio.h"
#include "emassert.h"
#include "util.h"
#include "transform.h"
#include <iostream>
#include <ctime>
#include <algorithm>

using namespace EMAN;

SpiderIO::SpiderIO(const string & spider_filename, IOMode rw)
:       filename(spider_filename), rw_mode(rw),
        spider_file(0), first_h(0), cur_h(0),
        is_big_endian(ByteOrder::is_host_big_endian()),
        initialized(false)
{
        is_new_file = !Util::is_file_exist(filename);
}

SpiderIO::~SpiderIO()
{
        if (spider_file) {
                fclose(spider_file);
                spider_file = 0;
        }

        if (first_h) {
                free(first_h);
                first_h = 0;
        }

        if (cur_h) {
                free(cur_h);
                cur_h = 0;
        }
}

void SpiderIO::init()
{
        if (initialized) {
                return;
        }
        ENTERFUNC;
        spider_file = sfopen(filename, rw_mode, &is_new_file);
        initialized = true;

        if (!is_new_file) {
                first_h = static_cast < SpiderHeader * >(calloc(1, sizeof(SpiderHeader)));

                if (fread(first_h, sizeof(SpiderHeader), 1, spider_file) != 1) {
                        throw ImageReadException(filename, "SPIDER header");
                }

                if (!is_valid_spider(first_h)) {
                        throw ImageReadException(filename, "invalid SPIDER");
                }

                float nslice = first_h->nslice;

                is_big_endian = ByteOrder::is_float_big_endian(nslice);
                become_host_endian((float *) first_h, NUM_FLOATS_IN_HEADER);

                if (first_h->istack == SINGLE_IMAGE_HEADER && rw_mode == WRITE_ONLY) {
                        fclose(spider_file);
                        spider_file = 0;

                        spider_file = fopen(filename.c_str(), "wb");
                }
        }

        EXITFUNC;
}

bool SpiderIO::is_valid_spider(const void *first_block)
{
        return SpiderIO::is_valid(first_block);
}

bool SpiderIO::is_valid(const void *first_block)
{
        ENTERFUNC;
        bool result = false;

        if (first_block) {
                const float *data = static_cast < const float *>(first_block);
                float nslice = data[0];
                float nrow = data[1];
                float iform = data[4];
                float nsam = data[11];
                float labrec = data[12];        //NO. of records in file header
                float labbyt = data[21];        //total NO. of bytes in header
                float lenbyt = data[22];        //record length in bytes
                float istack = data[23];

                bool big_endian = ByteOrder::is_float_big_endian(nslice);
                if (big_endian != ByteOrder::is_host_big_endian()) {
                        ByteOrder::swap_bytes(&nslice);
                        ByteOrder::swap_bytes(&nrow);
                        ByteOrder::swap_bytes(&iform);
                        ByteOrder::swap_bytes(&nsam);
                        ByteOrder::swap_bytes(&labrec);
                        ByteOrder::swap_bytes(&labbyt);
                        ByteOrder::swap_bytes(&lenbyt);
                        ByteOrder::swap_bytes(&istack);
                }

                if( int(nslice) != nslice || int(nrow) != nrow
                                || int(iform) != iform || int(nsam) != nsam
                                || int(labrec) != labrec || int(labbyt) != labbyt
                                || int(lenbyt) != lenbyt ) {
                        result =  false;
                }
                else {
                        //now we expect this header to be an overall header for SPIDER
                        if( int(istack) > 0 ) {
                                result = true; //istack>0 for overall header, istack<0 for indexed stack of image
                        }
                }

                int ilabrec = static_cast<int>(labrec);
                int ilabbyt = static_cast<int>(labbyt);
                int ilenbyt = static_cast<int>(lenbyt);
                if( ilabbyt != ilabrec * ilenbyt ) {
                        result = false;
                }
        }

        EXITFUNC;
        return result;
}

int SpiderIO::read_header(Dict & dict, int image_index, const Region * area, bool)
{
        ENTERFUNC;

    bool is_read_overall_header = false;
    if (image_index == -1) {
        is_read_overall_header = true;
        image_index = 0;
    }

        check_read_access(image_index);

        if (!first_h) {
                throw ImageReadException(filename, "empty spider header");
        }

        check_region(area, FloatSize(first_h->nsam, first_h->nrow,first_h->nslice), is_new_file,false);

        float size = first_h->nsam * first_h->nrow * first_h->nslice;
        int overall_headlen = 0;

    if (!is_read_overall_header) {
        if (first_h->istack > 0) {      //stack image
            overall_headlen = (int) first_h->headlen;
        }
        else if(first_h->istack == SINGLE_IMAGE_HEADER) {       //single 2D/3D image
            if(image_index != 0) {
                char desc[1024];
                sprintf(desc, "For a single image, index must be 0. Your image index = %d.", image_index);
                throw ImageReadException(filename, desc);
            }
        }
        else {  //complex spider image not supported
                throw ImageFormatException("complex spider image not supported.");
        }
    }

        size_t single_image_size = (size_t) (first_h->headlen + size * sizeof(float));
        size_t offset = overall_headlen + single_image_size * image_index;

        SpiderHeader *cur_image_hed;
        if (offset == 0) {
                cur_image_hed = first_h;
        }
        else {
                cur_image_hed = static_cast < SpiderHeader * >(calloc(1, sizeof(SpiderHeader)));
                portable_fseek(spider_file, offset, SEEK_SET);

                if (fread(cur_image_hed, sizeof(SpiderHeader), 1, spider_file) != 1) {
                        char desc[1024];
                        sprintf(desc, "read spider header with image_index = %d failed", image_index);
                        throw ImageReadException(filename, desc);
                }

                become_host_endian((float *) cur_image_hed, NUM_FLOATS_IN_HEADER);

                if (cur_image_hed->nsam != first_h->nsam || cur_image_hed->nrow != first_h->nrow
                        || cur_image_hed->nslice != first_h->nslice) {
                        char desc[1024];
                        sprintf(desc, "%dth image size %dx%dx%d != overall size %dx%dx%d",
                                        image_index, (int)cur_image_hed->nsam, (int)cur_image_hed->nrow,
                                        (int)cur_image_hed->nslice,
                                        (int)first_h->nsam, (int)first_h->nrow, (int)first_h->nslice);
                        throw ImageReadException(filename, desc);
                }
        }


        int xlen = 0, ylen = 0, zlen = 0;
        EMUtil::get_region_dims(area, (int) cur_image_hed->nsam, &xlen, (int) cur_image_hed->nrow,
                                                        &ylen, (int) cur_image_hed->nslice, &zlen);

        dict["nx"] = xlen;
        dict["ny"] = ylen;
        dict["nz"] = zlen;

        dict["datatype"] = EMUtil::EM_FLOAT;

        if(cur_image_hed->mmvalid == 1) {
                dict["minimum"] = cur_image_hed->min;
                dict["maximum"] = cur_image_hed->max;
                dict["mean"] = cur_image_hed->mean;
                dict["sigma"] = cur_image_hed->sigma;
        }

        dict["SPIDER.nslice"] = (int) cur_image_hed->nslice;
        dict["SPIDER.type"] = (int) cur_image_hed->type;

        dict["SPIDER.irec"] = cur_image_hed->irec;

        dict["SPIDER.angvalid"] = (int)cur_image_hed->angvalid;
        if((int)dict["SPIDER.angvalid"] != 0) {
                dict["SPIDER.phi"] = cur_image_hed->phi;
                dict["SPIDER.theta"] = cur_image_hed->theta;
                dict["SPIDER.gamma"] = cur_image_hed->gamma;
        }

        dict["SPIDER.headrec"] = (int) cur_image_hed->headrec;
        dict["SPIDER.headlen"] = (int) cur_image_hed->headlen;
        dict["SPIDER.reclen"] = (int) cur_image_hed->reclen;

        dict["SPIDER.dx"] = cur_image_hed->dx;
        dict["SPIDER.dy"] = cur_image_hed->dy;
        dict["SPIDER.dz"] = cur_image_hed->dz;

        dict["SPIDER.istack"] = (int) cur_image_hed->istack;
        if((int)dict["SPIDER.istack"] > 0) {    //maxim only for overall header
                dict["SPIDER.maxim"] = (int)cur_image_hed->maxim;
        }
        dict["SPIDER.imgnum"] = (int)cur_image_hed->imgnum;

        dict["SPIDER.Kangle"] = (int)cur_image_hed->Kangle;
        if((int)dict["SPIDER.Kangle"] == 1) {
                dict["SPIDER.phi1"] = cur_image_hed->phi1;
                dict["SPIDER.theta1"] = cur_image_hed->theta1;
                dict["SPIDER.psi1"] = cur_image_hed->psi1;
        }
        else if((int)dict["SPIDER.Kangle"] == 2) {
                dict["SPIDER.phi1"] = cur_image_hed->phi1;
                dict["SPIDER.theta1"] = cur_image_hed->theta1;
                dict["SPIDER.psi1"] = cur_image_hed->psi1;
                dict["SPIDER.phi2"] = cur_image_hed->phi2;
                dict["SPIDER.theta2"] = cur_image_hed->theta2;
                dict["SPIDER.psi2"] = cur_image_hed->psi2;
        }

        dict["SPIDER.date"] = string(cur_image_hed->date).substr(0, 11);
        dict["SPIDER.time"] = string(cur_image_hed->time).substr(0, 8);

        dict["SPIDER.title"] = string(cur_image_hed->title);

        if(cur_image_hed->scale>0) {
                dict["SPIDER.scale"] = cur_image_hed->scale;
                Dict dic;
                dic.put("type", "spider");
                dic.put("phi", cur_image_hed->phi);
                dic.put("theta", cur_image_hed->theta);
                dic.put("psi", cur_image_hed->gamma);
                dic.put("tx", cur_image_hed->dx);
                dic.put("ty", cur_image_hed->dy);
                dic.put("tz", cur_image_hed->dz);
                dic.put("scale", cur_image_hed->scale);
                Transform * trans = new Transform(dic);
                if(zlen<=1) {
                        dict["xform.projection"] = trans;
                }
                else {
                        dict["xform.align3d"] = trans;
                }
                if(trans) {delete trans; trans=0;}
        }


        if (offset != 0) {
                if( cur_image_hed )
                {
                        free(cur_image_hed);
                        cur_image_hed = 0;
                }
        }
        EXITFUNC;
        return 0;
}


int SpiderIO::write_header(const Dict & dict, int image_index, const Region* area,
                                                   EMUtil::EMDataType, bool use_host_endian)
{
        ENTERFUNC;

        if(is_new_file) {       //for a new file write overall header first
                write_single_header(dict, area, image_index, 0, first_h, OVERALL_STACK_HEADER, 1, 0, use_host_endian);
        }
        else {
                swap_header(first_h);
        }

        if(!initialized) {
                init();
        }

        if(!((int)dict["nx"]==first_h->nsam && (int)dict["ny"]==first_h->nrow &&
                        (int)dict["nz"]==first_h->nslice)) {
                char desc[1024];
                sprintf(desc, "%dth image size %dx%dx%d != overall size %dx%dx%d",
                                image_index, (int)dict["nx"], (int)dict["ny"], (int)dict["nz"],
                                (int)first_h->nsam, (int)first_h->nrow, (int)first_h->nslice);
                throw ImageReadException(filename, desc);
        }

        if (!cur_h) {
                cur_h = (SpiderHeader *) calloc(1, static_cast<size_t>(first_h->headlen));
        }

        int MAXIM;
        float size = first_h->nsam * first_h->nrow * first_h->nslice;
        size_t single_image_size = (int) (first_h->headlen + size * sizeof(float));
        size_t offset;
        if(image_index == -1) { //append image
                offset = (int) first_h->headlen + single_image_size * (int)first_h->maxim;
                MAXIM = (int)first_h->maxim + 1;
        }
        else {
                offset = (int) first_h->headlen + single_image_size * image_index;
                MAXIM = image_index>=(int)first_h->maxim ? image_index+1 : (int)first_h->maxim;
        }

        //update overall header
        if(MAXIM > (int)first_h->maxim) {
                portable_fseek(spider_file, 0, SEEK_SET);
                write_single_header(dict, area, image_index, 0, first_h, OVERALL_STACK_HEADER, MAXIM, 0, use_host_endian);
        }

        portable_fseek(spider_file, offset, SEEK_SET);
        write_single_header(dict, area, image_index, offset, cur_h, SINGLE_IMAGE_HEADER, 0, image_index+1, use_host_endian);

        EXITFUNC;
        return 0;
}

int SpiderIO::write_single_header(const Dict & dict, const Region *area, int image_index, size_t offset,
                                        SpiderHeader *& hp, int ISTACK, int MAXIM, int IMGNUM, bool use_host_endian)
{
        ENTERFUNC;

        check_write_access(rw_mode, image_index);

        if (area) {
                check_region(area, FloatSize(hp->nsam, hp->nrow, hp->nslice), is_new_file);
                EXITFUNC;
                return 0;
        }

        int nx = dict["nx"];
        int ny = dict["ny"];
        int nz = dict["nz"];

        size_t header_size = sizeof(SpiderHeader);
        size_t record_size = nx * sizeof(float);
    size_t num_records = (header_size % record_size) == 0 ? header_size / record_size : header_size / record_size + 1;
        size_t header_length = num_records * record_size;

        if (!hp) {
                hp = static_cast < SpiderHeader * >(calloc(1, header_size));
        }

        hp->angvalid = 0;
        hp->scale = 1.0;
        hp->istack = (float)ISTACK;
        hp->nslice = (float)nz;
        hp->nsam = (float)nx;
        hp->nrow = (float)ny;

        hp->max = dict["maximum"];
        hp->min = dict["minimum"];
        hp->mean = dict["mean"];
        hp->sigma = dict["sigma"];
        hp->mmvalid = 1;

        if(nz<=1 && dict.has_key("xform.projection")) {
                hp->angvalid = 1;
                Transform * t = dict["xform.projection"];
                Dict d = t->get_params("spider");
                hp->phi = d["phi"];
                hp->theta = d["theta"];
                hp->gamma = d["psi"];
                hp->dx = d["tx"];
                hp->dy = d["ty"];
                hp->dz = d["tz"];
                hp->scale = d["scale"];
                if(t) {delete t; t=0;}
        }
        else if(nz>1 && dict.has_key("xform.align3d")) {
                hp->angvalid = 1;
                Transform * t = dict["xform.align3d"];
                Dict d = t->get_params("spider");
                hp->phi = d["phi"];
                hp->theta = d["theta"];
                hp->gamma = d["psi"];
                hp->dx = d["tx"];
                hp->dy = d["ty"];
                hp->dz = d["tz"];
                hp->scale = d["scale"];
                if(t) {delete t; t=0;}
        }

        if(nz == 1) {
                hp->type = IMAGE_2D;
        }
        else {
                hp->type = IMAGE_3D;
        }

// complex image file not supported in EMAN2

        hp->reclen = (float)record_size;
        hp->headrec = (float)num_records;
        hp->headlen = (float)header_length;

        if(ISTACK == OVERALL_STACK_HEADER) {
                hp->maxim = (float)MAXIM;
        }
        hp->irec = (float)(num_records + ny*nz);

        hp->imgnum = (float)IMGNUM;

        time_t tod;
        time(&tod);
        struct tm * ttt = localtime(&tod);
        char ctime[9];
        char cdate[12];
        strftime(ctime, 9, "%H:%M:%S", ttt);
        std::copy(&ctime[0], &ctime[8], hp->time);
        strftime(cdate, 12, "%d-%b-%Y", ttt);
        std::copy(&cdate[0], &cdate[11], hp->date);

        if(dict.has_key("SPIDER.title")) {
                string title = static_cast<string>(dict["SPIDER.title"]);
                std::copy(&(title[0]), &(title[title.length()]), hp->title);
        }

        portable_fseek(spider_file, offset, SEEK_SET);

        if(use_host_endian) {
                if (fwrite(hp, header_size, 1, spider_file) != 1) {
                        throw ImageWriteException(filename, "write spider header failed");
                }
        }
        else {  //swap byte order
                SpiderHeader * hp2 = new SpiderHeader(*hp);
                ByteOrder::swap_bytes((float *) hp2, NUM_FLOATS_IN_HEADER);
                if (fwrite(hp2, header_size, 1, spider_file) != 1) {
                        throw ImageWriteException(filename, "write spider header failed");
                }
                if(hp2) {delete hp2; hp2=0;}
        }

        size_t pad_size = header_length - header_size;
        char *pad = static_cast < char *>(calloc(pad_size, 1));
        fwrite(pad, pad_size, 1, spider_file);
        if( pad )
        {
                free(pad);
                pad = 0;
        }

        EXITFUNC;
        return 0;
}


int SpiderIO::read_data(float *data, int image_index, const Region * area, bool)
{
        ENTERFUNC;

        check_read_access(image_index, data);

        check_region(area, FloatSize((int) first_h->nsam, (int) first_h->nrow,
                                                                 (int) first_h->nslice), is_new_file,false);

        int overall_headlen = 0;
        if (first_h->istack >0) {       //for over all header length
                overall_headlen = (int) first_h->headlen;
        }
        else {
                if(image_index != 0) {
                        char desc[256];
                        sprintf(desc, "For single image, index must be 0. Your image index = %d.", image_index);
                        throw ImageReadException(filename, desc);
                }
        }

        size_t size = static_cast < size_t > (first_h->nsam * first_h->nrow * first_h->nslice);
        size_t single_image_size = static_cast < size_t > (first_h->headlen + size * sizeof(float));
        off_t offset = overall_headlen + single_image_size * image_index;
        portable_fseek(spider_file, offset, SEEK_SET);

        portable_fseek(spider_file, (int) first_h->headlen, SEEK_CUR);

#if 1
        EMUtil::process_region_io(data, spider_file, READ_ONLY, 0, sizeof(float),
                                                          (int) first_h->nsam, (int) first_h->nrow,
                                                          (int) first_h->nslice, area);
#endif
#if 0
        unsigned int nz = static_cast < unsigned int >(first_h->nslice);
        int sec_size = static_cast < int >(first_h->nsam * first_h->nrow * sizeof(float));

        if (fread(data, sec_size, nz, spider_file) != nz) {
                LOGERR("Incomplete SPIDER data read");
                return 1;
        }
#endif

        int xlen = 0, ylen = 0, zlen = 0;
        EMUtil::get_region_dims(area, (int) first_h->nsam, &xlen, (int) first_h->nrow, &ylen,
                                                        (int) first_h->nslice, &zlen);

        int data_size = xlen * ylen * zlen;
        become_host_endian(data, data_size);
        EXITFUNC;
        return 0;
}

int SpiderIO::write_data(float *data, int image_index, const Region* area,
                                                 EMUtil::EMDataType, bool use_host_endian)
{
        ENTERFUNC;

        if(!cur_h) {
                throw ImageWriteException(filename, "Please write header before write data");
        }

        if(first_h->istack == SINGLE_IMAGE_HEADER) {
                throw ImageWriteException(filename, "Cannot mix single spider and stack spider");
        }

        size_t offset;
        float size = first_h->nsam * first_h->nrow * first_h->nslice;
        size_t single_image_size = (int) (first_h->headlen + size * sizeof(float));
        offset = (int) first_h->headlen + single_image_size * image_index + (int) first_h->headlen;

        swap_data(data, (size_t)size);

        write_single_data(data, area, cur_h, offset, image_index, (int)first_h->maxim+1, use_host_endian);

        EXITFUNC;
        return 0;
}


void SpiderIO::flush()
{
        fflush(spider_file);
}

int SpiderIO::write_single_data(float *data, const Region * area, SpiderHeader *& hp,
                                                                size_t offset, int img_index, int max_nimg, bool use_host_endian)
{
        ENTERFUNC;

        check_write_access(rw_mode, img_index, max_nimg, data);

        if (area) {
                check_region(area, FloatSize(hp->nsam, hp->nrow, hp->nslice), is_new_file);
        }

        if (!hp) {
                throw ImageWriteException(filename, "NULL image header");
        }

        portable_fseek(spider_file, offset, SEEK_SET);

        int size = (int)(hp->nsam * hp->nrow * hp->nslice);
        if(!use_host_endian) {
                ByteOrder::swap_bytes(data, size);
        }

        // remove the stuff in #if 0 ... #endif if the following works.
        EMUtil::process_region_io(data, spider_file, WRITE_ONLY,0, sizeof(float),
                                                          (int) hp->nsam, (int) hp->nrow,
                                                          (int) hp->nslice, area);

        EXITFUNC;
        return 0;
}

void SpiderIO::swap_data(float *data, size_t size)
{
        if (data && need_swap()) {
                ByteOrder::swap_bytes(data, size);
        }
}

void SpiderIO::swap_header(SpiderHeader * header)
{
        if (header && need_swap()) {
                ByteOrder::swap_bytes((float *) header, NUM_FLOATS_IN_HEADER);
        }
}

bool SpiderIO::is_complex_mode()
{
        int type = static_cast<int>(first_h->type);
        if (type == IMAGE_2D_FFT_ODD
                || type == IMAGE_2D_FFT_EVEN
                || type == IMAGE_3D_FFT_ODD
                || type == IMAGE_3D_FFT_EVEN
           ) return true;
        return false;
}

bool SpiderIO::is_image_big_endian()
{
        init();
        return is_big_endian;
}

int SpiderIO::get_nimg()
{
        init();
        if (!first_h) {
                Assert(is_new_file);
                return 0;
        }
        else if (first_h->istack > 0) {                                         //image stack
                return static_cast < int >(first_h->maxim);
        }
        else if (first_h->istack == SINGLE_IMAGE_HEADER) {      //single 2D/3D image
                return 1;
        }
        else {                                                                                          //complex image
                throw ImageFormatException("complex spider image not supported.");
        }
}

bool SpiderIO::need_swap() const
{
        if (!is_new_file && (is_big_endian != ByteOrder::is_host_big_endian())) {
                return true;
        }
        return false;
}
/* vim: set ts=4 noet: */