dm4io.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 "dm4io.h"
#include "portable_fileio.h"
#include "geometry.h"
 
using namespace EMAN;
using namespace EMAN::GatanDM4;
 
const char *TagTable::IMAGE_WIDTH_TAG = "Dimensions #0";
const char *TagTable::IMAGE_HEIGHT_TAG = "Dimensions #1";
const char *TagTable::IMAGE_NIMG_TAG = "Dimensions #2";
const char *TagTable::IMAGE_DATATYPE_TAG = "DataType";
const char *TagTable::IMAGE_THUMB_INDEX_TAG = "ImageIndex";
 
 
TagTable::TagTable()
        :       img_index(0), is_big_endian(true), img_counted(1), num_images_found(0)
{
}
 
TagTable::~TagTable()
{
        for (unsigned int i = 0; i < data_list.size(); i++) {
                if (data_list[i]) {
                        delete[]data_list[i];
                        data_list[i] = 0;
                }
        }
}
 
void TagTable::add(const string & name, const string & value)
{
        const char *value_str = value.c_str();
 
        if (name == IMAGE_WIDTH_TAG) {
                x_list.push_back(atoi(value_str));
        }
        else if (name == IMAGE_HEIGHT_TAG) {
                y_list.push_back(atoi(value_str));
        }
        else if (name == IMAGE_DATATYPE_TAG) {
                datatype_list.push_back(atoi(value_str));
        }
        else if (name == IMAGE_THUMB_INDEX_TAG) {
                set_thumb_index(atoi(value_str));
        }
        else if(name == IMAGE_NIMG_TAG){
                img_counted=atoi(value_str);
        }
        else {
                tags[name] = value;
        }
}
 
void TagTable::add_data(char *data)
{
        if (!data) {
                throw NullPointerException("DM4 data is NULL");
        }
        else {
                data_list.push_back(data);
        }
}
 
string TagTable::get_string(const string & name)
{
        return tags[name];
}
 
int TagTable::get_int(const string & name)
{
        return atoi(tags[name].c_str());
}
 
float TagTable::get_float(const string & name)
{
        return static_cast < float >(atof(tags[name].c_str()));
}
 
double TagTable::get_double(const string & name)
{
        return atof(tags[name].c_str());
}
 
void TagTable::dump() const
{
        map < string, string >::const_iterator p;
 
        for (p = tags.begin(); p != tags.end(); p++) {
//              LOGDEBUG("  %s: %s", (*p).first.c_str(), (*p).second.c_str());
                printf("  %s: %s\n", (*p).first.c_str(), (*p).second.c_str());
        }
}
 
int TagTable::get_xsize() const
{
        return x_list[img_index];
}
 
int TagTable::get_image_counted() const
{
        return img_counted;
}
 
int TagTable::get_ysize() const
{
        return y_list[img_index];
}
 
int TagTable::get_datatype() const
{
        return datatype_list[img_index];
}
 
char *TagTable::get_data() const
{
        return data_list[img_index];
}
 
void TagTable::set_thumb_index(int i)
{
        if (i != 0 && i != 1) {
                throw OutofRangeException(0, 1, i, "image index");
        }
        else {
                if (i == 0) {
                        img_index = 1;
                }
                else {
                        img_index = 0;
                }
        }
}
 
int TagTable::get_num_images_found() const
{
        return num_images_found;
}
 
void TagTable::set_num_images_found(int num_found)
{
        num_images_found = num_found;
}
 
 
TagData::TagData(FILE * data_file, TagTable * table, const string & tagname)
        :       in(data_file), tagtable(table), name(tagname), tag_type(UNKNOWN)
{
}
 
TagData::~TagData()
{
}
 
string TagData::read_native(bool is_value_stored)
{
        size_t sz = typesize();
        size_t nr;
        char val_str[32];
 
        if (tag_type == SHORT) {
                short val = 0;
                nr = fread(&val, sz, 1, in); nr++;
                tagtable->become_host_endian(&val);
                sprintf(val_str, "%d", val);
        }
        else if (tag_type == USHORT) {
                unsigned short val = 0;
                nr = fread(&val, sz, 1, in); nr++;
                tagtable->become_host_endian(&val);
                sprintf(val_str, "%d", val);
        }
        else if (tag_type == INT) {
                int val = 0;
                nr = fread(&val, sz, 1, in); nr++;
                tagtable->become_host_endian(&val);
                sprintf(val_str, "%d", val);
        }
        else if (tag_type == CHAR || tag_type == OCTET) {
                char val = 0;
                nr = fread(&val, sz, 1, in); nr++;
                sprintf(val_str, "%d", val);
        }
        else if (tag_type == BOOLEAN) {
                bool val = false;
                nr = fread(&val, sz, 1, in); nr++;
                tagtable->become_host_endian(&val);
                sprintf(val_str, "%d", val);
        }
        else if (tag_type == UINT) {
                unsigned int val = 0;
                nr = fread(&val, sz, 1, in); nr++;
                tagtable->become_host_endian(&val);
                sprintf(val_str, "%u", (int) val);
        }
        else if (tag_type == FLOAT) {
                float val = 0;
                nr = fread(&val, sz, 1, in); nr++;
                tagtable->become_host_endian(&val);
                sprintf(val_str, "%f", val);
        }
        else if (tag_type == DOUBLE) {
                double val = 0;
                nr = fread(&val, sz, 1, in); nr++;
                tagtable->become_host_endian(&val);
                sprintf(val_str, "%10e", val);
        }
        else if (tag_type == OCTEU) {
                long long val = 0;
                nr = fread(&val, sz, 1, in); nr++;
                tagtable->become_host_endian(&val);
                sprintf(val_str, "%lld", val);
        }
        else if (tag_type == OCTEV) {
                unsigned long long val = 0;
                nr = fread(&val, sz, 1, in); nr++;
                tagtable->become_host_endian(&val);
                sprintf(val_str, "%lld", val);
        }
        else {
                LOGERR("invalid tag type: '%lld'", tag_type);
                exit(1);
        }
 
        if (is_value_stored) {
                tagtable->add(name, val_str);
        }
 
        LOGVAR("value = '%s'", val_str);
 
        return string(val_str);
}
 
vector < int >TagData::read_array_types()
{
        LOGVAR("TagData::read_array_types()");
 
        long long array_type = 0;
        size_t nr;
        nr = fread(&array_type, sizeof(array_type), 1, in); nr++;
 
        ByteOrder::become_big_endian(&array_type);
 
        LOGVAR("array data type = '%s'", GatanDM4::to_str((Type) array_type));
 
        vector < int >item_types;
 
        if (array_type == STRUCT) {
                item_types = read_struct_types();
        }
        else if (array_type == ARRAY) {
                item_types = read_array_types();
                LOGERR("DM4: don't know how to handle this array type");
        }
        else {
                item_types.push_back(array_type);
        }
 
        return item_types;
}
 
// string tag data are stored in unicode
string TagData::read_string(int size)
{
        if (size <= 0) {
                return string("");
        }
 
        unsigned short *buf = new unsigned short[size];
        char *str = new char[size + 1];
 
        size_t nr;
        nr = fread(buf, size * sizeof(unsigned short), 1, in); nr++;
        tagtable->become_host_endian < unsigned short >(buf, size);
 
        for (int i = 0; i < size; i++) {
                str[i] = static_cast < char >(buf[i]);
        }
 
        str[size] = '\0';
        string str1 = string(str);
 
        if (str) {
                delete [] str;
                str = NULL;
        }
 
        if (buf) {
                delete [] buf;
                buf = NULL;
        }
 
        return str1;
}
 
int TagData::read_array_data(vector < int >item_types, bool nodata, int image_index, int num_images)
{
        ENTERFUNC;
        if (item_types.size() == 0) {
                LOGERR("DM4 item types cannot be empty");
                return 1;
        }
 
        int err = 0;
        long long array_size = 0;
 
        size_t nr;
        nr = fread(&array_size, sizeof(array_size), 1, in); nr++;
        ByteOrder::become_big_endian(&array_size);
 
        LOGVAR("array size = %lld\n", array_size);
 
        size_t item_size = 0;
        for (size_t i = 0; i < item_types.size(); i++) {
                item_size += typesize(item_types[i]);
        }
 
        LOGVAR("%s array item size = %lld\n", name.c_str(), item_size);
 
        size_t buf_size = item_size * array_size;
 
        if (item_types.size() == 1 && item_types[0] == USHORT && nodata) {
                string val = read_string(array_size);
                tagtable->add(name, val);
                LOGVAR("value: %s", val.c_str());
        }
        else if (!nodata && name == "Data") {
                int num_found = tagtable->get_num_images_found();
                num_found++;
                tagtable->set_num_images_found(num_found);
 
                char * data;
 
                if (image_index < 0  ||  buf_size % num_images != 0  ||  num_found == 1) {
                        data = new char[buf_size];
                        nr = fread(data, item_size, array_size, in); nr++;
                }
                else {
                        size_t image_size = buf_size / num_images;
 
                        data = new char[image_size];
                        portable_fseek(in, image_index * image_size, SEEK_CUR);
                        nr = fread(data, image_size, 1, in); nr++;
                        portable_fseek(in, (num_images - image_index - 1) * image_size, SEEK_CUR);
                        array_size = array_size / num_images;
                }
 
                if (item_size == sizeof(short)) {
                        tagtable->become_host_endian((short *) data, array_size);
                }
                else if (item_size == sizeof(int)) {
                        tagtable->become_host_endian((int *) data, array_size);
                }
                else if (item_size == sizeof(double)) {
                        tagtable->become_host_endian((double *) data, array_size);
                }
                else {
                        LOGERR("cannot handle this type of DM4 image data");
                        return 1;
                }
 
                tagtable->add_data(data);
        }
        else {
                portable_fseek(in, buf_size, SEEK_CUR);
        }
        EXITFUNC;
        return err;
}
 
vector < int >TagData::read_struct_types()
{
        LOGVAR("TagData::read_struct_types()");
 
        long long namelength = 0;
        long long nfields = 0;
 
        size_t nr;
        nr = fread(&namelength, sizeof(namelength), 1, in); nr++;
        ByteOrder::become_big_endian(&namelength);
 
        nr = fread(&nfields, sizeof(nfields), 1, in); nr++;
        ByteOrder::become_big_endian(&nfields);
 
        LOGVAR("namelength = %lld\n", namelength);
        LOGVAR("num fields = %lld\n", nfields);
 
        vector < int >field_types;
 
        for (unsigned int i = 0; i < nfields; i++) {
                nr = fread(&namelength, sizeof(namelength), 1, in); nr++;
                ByteOrder::become_big_endian(&namelength);
 
                long long field_type = 0;
                nr = fread(&field_type, sizeof(field_type), 1, in); nr++;
                ByteOrder::become_big_endian(&field_type);
                
                LOGVAR("%dth namelength = %lld, type = '%s'",
                           i, namelength, GatanDM4::to_str((Type) field_type));
                field_types.push_back(field_type);
        }
 
        return field_types;
}
 
int TagData::read_any(bool nodata, int image_index, int num_images)
{
        int err = 0;
 
        size_t nr;
        nr = fread(&tag_type, sizeof(tag_type), 1, in); nr++;
        
        ByteOrder::become_big_endian(&tag_type);
        LOGVAR("TagData::read_any tag type = '%s'\n", GatanDM4::to_str((Type) tag_type));
 
 
        if (tag_type == ARRAY) {
                vector < int >item_types = read_array_types();
                err = read_array_data(item_types, nodata, image_index, num_images);
        }
        else if (tag_type == STRUCT) {
                vector < int >field_types = read_struct_types();
 
                for (unsigned int i = 0; i < field_types.size(); i++) {
                        
                        tag_type = static_cast < Type > (field_types[i]);
                        
                        string val = read_native(false);
                        
                        char int_str[32];
                        sprintf(int_str, " #%d", i);
                        string fieldname = name + string(int_str);
                        tagtable->add(fieldname, val);
                }
        }
        else if (tag_type == STRING) {
 
                int str_sz = 0;
                size_t nr;
                nr = fread(&str_sz, sizeof(str_sz), 1, in); nr++;
                ByteOrder::become_big_endian(&str_sz);
 
                char *val = new char[str_sz + 1];
                nr = fread(val, str_sz, 1, in); nr++;
                val[str_sz] = '\0';
                string val_str = string(val);
 
                if (val) {
                        delete [] val;
                        val = NULL;
                }
 
                tagtable->add(name, val_str);
        }
        else {
                read_native(true);
        }
 
        return err;
}
 
int TagData::read_tag_data(bool nodata, int image_index, int num_images)
{
        LOGVAR("TagData::read_tag_data()");
        int err = 0;
 
        const char *DATA_TYPE_MARK = "%%%%";
        const size_t mark_sz = strlen(DATA_TYPE_MARK);
        char *mark = new char[mark_sz + 1];
 
        long long interval;
        
        size_t nr;
        nr = fread(&interval, sizeof(interval), 1, in); nr++;
 
        ByteOrder::become_big_endian(&interval);
 
        nr = fread(mark, mark_sz, 1, in); nr++;
        mark[mark_sz] = '\0';
 
        if (strcmp(mark, DATA_TYPE_MARK) != 0) {
                LOGERR("data type label has been changed from '%s' to '%s'",
                           DATA_TYPE_MARK, mark);
                return 1;
        }
 
        if (mark) {
                delete [] mark;
                mark = NULL;
        }
 
        long long encoded_types_size = 0;
        nr = fread(&encoded_types_size, sizeof(long long), 1, in); nr++;
        ByteOrder::become_big_endian(&encoded_types_size);
 
        LOGVAR("encoded types size = %lld\n", encoded_types_size);
 
        err = read_any(nodata, image_index, num_images);
 
        return err;
}
 
size_t TagData::typesize() const
{
        return typesize((int) tag_type);
}
 
size_t TagData::typesize(int t) const
{
        size_t size = 0;
        Type type = static_cast < Type > (t);
 
        
        switch (type) {
        case SHORT:
                size = sizeof(short);
                break;
        case USHORT:
                size = sizeof(unsigned short);
                break;
        case INT:
                size = sizeof(int);
                break;
        case UINT:
                size = sizeof(unsigned int);
                break;
        case FLOAT:
                size = sizeof(float);
                break;
        case DOUBLE:
                size = sizeof(double);
                break;
        case BOOLEAN:
                size = sizeof(bool);
                break;
        case CHAR:
        case OCTET:
                size = sizeof(char);
                break;
        case OCTEU:
                size = sizeof(double);
                break;
        case OCTEV:
                size = sizeof(double);
                break;
        default:
                LOGERR("no such type: '%d'\n", type);
                break;
        }
 
        return size;
}
 
 
TagEntry::TagEntry(FILE * data_file, TagTable * table, TagGroup * parent)
        :       in(data_file), tagtable(table), parent_group(parent), name("")
{
}
 
TagEntry::~TagEntry()
{
}
 
int TagEntry::read_tag_entry(bool nodata, int image_index, int num_images)
{
        LOGVAR("TagEntry::read_tag_entry()");
        int err = 0;
        long long pos = 0;
        char tagtype = 0;
        char *tmp_name = 0;
 
        pos = ftell(in);
        size_t nr;
        nr = fread(&tagtype, sizeof(char), 1, in); nr++;
 
        if (tagtype != GROUP_TAG && tagtype != DATA_TAG) {
                portable_fseek(in, sizeof(char) * 7, SEEK_CUR);
                nr = fread(&tagtype, sizeof(char), 1, in); nr++;
        }
 
        if (tagtype != GROUP_TAG && tagtype != DATA_TAG) {
                tagtype = fgetc(in);
                if (tagtype == EOF)
                {
                        return 1;
                }
                else{
                        LOGERR("TagEntry::read_tag_entry() invalid tag type: %d @ position %lld", tagtype, pos);
                        return 1;
                }
        }
 
        short name_len = 0;
        nr = fread(&name_len, sizeof(short), 1, in); nr++;
 
        ByteOrder::become_big_endian(&name_len);
 
        if (name_len != 0) {
                tmp_name = new char[name_len + 1];
                nr = fread(tmp_name, name_len, 1, in); nr++;
                tmp_name[name_len] = '\0';
        }
        else {
                string parent_name = parent_group->get_name();
                name_len = static_cast < short >(parent_name.size() + 4);
                tmp_name = new char[name_len + 1];
                sprintf(tmp_name, "%s #%d", parent_name.c_str(), parent_group->get_entry_id());
        }
 
        name = string(tmp_name);
 
        if (tmp_name) {
                delete [] tmp_name;
                tmp_name = NULL;
        }
 
        LOGVAR("\ntag name: '%s', len: %d, type: '%s'",
                   name.c_str(), name_len, GatanDM4::to_str((EntryType) tagtype));
 
        if (tagtype == DATA_TAG) {
                TagData tag_data(in, tagtable, name);
                err = tag_data.read_tag_data(nodata, image_index, num_images);
        }
        else if (tagtype == GROUP_TAG) {
                long long tot_size = 0; //size of DataType record + size of data
                nr = fread(&tot_size, sizeof(long long), 1, in); nr++;
                ByteOrder::become_big_endian(&tot_size);
 
                TagGroup group(in, tagtable, name);
                err = group.read_tag_group(nodata, image_index, num_images);
        }
 
/*
        long long tot_size = 0; //size of DataType record + size of data
        nr = fread(&tot_size, sizeof(long long), 1, in); nr++;
*/
        return err;
}
 
 
TagGroup::TagGroup(FILE * data_file, TagTable * table, const string & groupname)
        :       in(data_file), tagtable(table), name(groupname), entry_id(0)
{
}
 
TagGroup::~TagGroup()
{
}
 
int TagGroup::read_tag_group(bool nodata, int image_index, int num_images)
{
        LOGVAR("TagGroup::read_tag_group()");
        char is_sorted, is_open;
 
        long long ntags = 0;
        
//      portable_fseek(in, sizeof(char) * 2, SEEK_CUR);
        size_t nr;
        nr = fread(&is_sorted, sizeof(is_sorted), 1, in); nr++;
        nr = fread(&is_open,   sizeof(is_open),   1, in); nr++;
 
        nr = fread(&ntags, sizeof(ntags), 1, in); nr++;
        
        ByteOrder::become_big_endian(&ntags);
 
        LOGVAR("DM4: ntags = %d\n", ntags);
        
        int err = 0;
        // char flagend;
        for (int i = 0; i < ntags; i++) {
                /*
                portable_fseek(in, sizeof(char) * 9, SEEK_CUR);
                nr = fread(&flagend, sizeof(char), 1, in); nr++;
                
                if (flagend ==EOF){
                        break;
                }
                else{
                        portable_fseek(in, -sizeof(char) * 10, SEEK_CUR);;
                }
                
                */
                
                TagEntry tag_entry(in, tagtable, this);
                err = tag_entry.read_tag_entry(nodata, image_index, num_images);
 
                if (err) {
                        break;
                }
        }
 
        return err;
}
 
string TagGroup::get_name() const
{
        return name;
}
 
int TagGroup::get_entry_id()
{
        int id = entry_id;
        entry_id++;
        return id;
}
 
 
DM4IO::DM4IO(const string & fname, IOMode rw)
        :       ImageIO(fname, rw)
{
        is_big_endian = ByteOrder::is_host_big_endian();
        tagtable = new TagTable();
}
 
DM4IO::~DM4IO()
{
        if (file) {
                fclose(file);
                file = 0;
        }
        if (tagtable) {
                delete tagtable;
                tagtable = 0;
        }
}
 
void DM4IO::init()
{
        ENTERFUNC;
        if (initialized) {
                return;
        }
        initialized = true;
 
        if (rw_mode != READ_ONLY) {
                throw ImageReadException(filename, "only support DM4 read-only");
        }
 
        file = sfopen(filename, READ_ONLY);
 
        int stream_version = 0;
        if (fread(&stream_version, sizeof(stream_version), 1, file) != 1) {
                throw ImageReadException(filename, "read stream version of DM4 file");
        }
 
        long long recsize;
        if (fread(&recsize, sizeof(recsize), 1, file) != 1) {
                throw ImageReadException(filename, "read size of TagGroup recoed of DM4 file");
        }
 
        int endianness;
        if (fread(&endianness, sizeof(endianness), 1, file) != 1) {
                throw ImageReadException(filename, "read endianness indicator of DM4 file");
        }
 
        if (ByteOrder::is_data_big_endian(&stream_version) != ByteOrder::is_host_big_endian()) {
                ByteOrder::swap_bytes(&stream_version);
                ByteOrder::swap_bytes(&recsize);
                ByteOrder::swap_bytes(&endianness);
        }
 
        if (endianness == 0) {
                is_big_endian = true;
        }
        else {
                is_big_endian = false;
        }
 
        tagtable->set_endian(is_big_endian);
        
        LOGDEBUG("dm4 ver = %d, image size = %d, is_big_endian = %d",
                        stream_version, recsize, (int) is_big_endian);
 
        EXITFUNC;
}
 
bool DM4IO::is_valid(const void *first_block)
{
        ENTERFUNC;
 
        if (!first_block) {
                return false;
        }
 
        const int *data = static_cast < const int *>(first_block);
 
        int img_ver = data[0];
        int byte_order = data[3];
        if (ByteOrder::is_data_big_endian(&img_ver) != ByteOrder::is_host_big_endian()) {
                ByteOrder::swap_bytes(&img_ver);
                ByteOrder::swap_bytes(&byte_order);
        }
 
        if (img_ver != 4) {
                return false;
        }
 
        if (byte_order != 0 && byte_order != 1) {
                return false;
        }
 
        return true;
}
 
bool DM4IO::is_image_big_endian()
{
        init();
        return is_big_endian;
}
 
int DM4IO::read_header(Dict & dict, int image_index, const Region * area, bool)
{
        ENTERFUNC;
        int err = 0;
 
        //single image format, index can only be zero
        if(image_index == -1) {
                image_index = 0;
        }
        image_index = 0;
        check_read_access(image_index);
 
        portable_fseek(file, NUM_ID_INT * sizeof(int), SEEK_SET);
        TagGroup root_group(file, tagtable, "");
        root_group.read_tag_group(true, 0, 1);
 
        int nx = tagtable->get_xsize();
        int ny = tagtable->get_ysize();
 
        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["nimg"] = tagtable->get_image_counted();
        dict["DM4.acq_date"] = tagtable->get_string("Acquisition Date");
        dict["DM4.acq_time"] = tagtable->get_string("Acquisition Time");
        dict["DM4.source"] = tagtable->get_string("Source");
        dict["DM4.exposure_number"] = tagtable->get_int("Exposure Number");
        dict["DM4.exposure_time"] = tagtable->get_double("Exposure (s)");
        dict["DM4.zoom"] = tagtable->get_double("Zoom");
        dict["DM4.antiblooming"] = tagtable->get_int("Antiblooming");
        dict["DM4.indicated_mag"] = tagtable->get_double("Indicated Magnification");
        dict["DM4.actual_mag"] = tagtable->get_double("Actual Magnification");
        dict["DM4.pixel_size"] = tagtable->get_double("Pixel Size (um) #0");
        dict["DM4.name"] = tagtable->get_string("Name");
 
        dict["DM4.voltage"] = tagtable->get_double("Voltage")/1000.0;
        dict["microscope_voltage"]=(float)dict["DM4.voltage"];
        dict["DM4.cs"] = tagtable->get_double("Cs(mm)");
        dict["microscope_cs"]=(float)dict["DM4.cs"];
 
        dict["DM4.frame_type"] = tagtable->get_string("Processing");
        dict["DM4.camera_x"] = tagtable->get_int("Active Size (pixels) #0");
        dict["DM4.camera_y"] = tagtable->get_int("Active Size (pixels) #1");
        dict["DM4.binning_x"] = tagtable->get_int("Binning #0");
        dict["DM4.binning_y"] = tagtable->get_int("Binning #1");
        dict["datatype"] = to_em_datatype(tagtable->get_datatype());
 
        if ((float)dict["DM4.actual_mag"] >0.0) {
                float apix=10000.0*(float)dict["DM4.pixel_size"]/(float)dict["DM4.actual_mag"];
                dict["apix_x"]=apix;
                dict["apix_y"]=apix;
                dict["apix_z"]=apix;
        }
 
        EXITFUNC;
        return err;
}
 
int DM4IO::read_data(float *rdata, int image_index, const Region * area, bool)
{
        ENTERFUNC;
 
        check_read_access(image_index, rdata);
 
        portable_fseek(file, NUM_ID_INT * sizeof(int), SEEK_SET);
        TagGroup root_group(file, tagtable, "");
        root_group.read_tag_group(true, 0, 1);
 
        int nx = tagtable->get_xsize();
        int ny = tagtable->get_ysize();
        int num_images = tagtable->get_image_counted();
 
        portable_fseek(file, NUM_ID_INT * sizeof(int), SEEK_SET);
        root_group.read_tag_group(false, image_index, num_images);
 
        check_region(area, IntSize(nx, ny));
 
        int xlen = 0, ylen = 0, x0 = 0, y0 = 0;
        EMUtil::get_region_dims(area, nx, &xlen, ny, &ylen);
        EMUtil::get_region_origins(area, &x0, &y0);
 
        char *data = tagtable->get_data();
        int data_type = tagtable->get_datatype();
 
        long long offset = 0;
        long long k = 0;
        long long off = 0;
        int xlast = x0 + xlen;
        int ylast = y0 + ylen;
 
//      bool flip_vertical = (getenv ("FLIP_VERTICAL") != NULL);
        bool flip_vertical = true;
 
        for (int iy = y0; iy < ylast; iy++) {
                if (flip_vertical) {
                        off = offset + (y0 + ylast - 1 - iy) * nx;
                }
                else {
                        off = offset + iy * nx;
                }
 
                switch (data_type) {
                case GatanDM4::DataType::SIGNED_INT8_DATA:
                        for (int ix = x0; ix < xlast; ix++) {
                                rdata[k] = (float) ((char *) data)[off + ix];
                                k++;
                        }
                        break;
                case GatanDM4::DataType::UNSIGNED_INT8_DATA:
                        for (int ix = x0; ix < xlast; ix++) {
                                rdata[k] = (float) ((unsigned char *) data)[off + ix];
                                k++;
                        }
                        break;
                case GatanDM4::DataType::SIGNED_INT16_DATA:
                        for (int ix = x0; ix < xlast; ix++) {
                                rdata[k] = (float) ((short *) data)[off + ix];
                                k++;
                        }
                        break;
                case GatanDM4::DataType::UNSIGNED_INT16_DATA:
                        for (int ix = x0; ix < xlast; ix++) {
                                rdata[k] = (float) ((unsigned short *) data)[off + ix];
                                k++;
                        }
                        break;
                case GatanDM4::DataType::SIGNED_INT32_DATA:
                        for (int ix = x0; ix < xlast; ix++) {
                                rdata[k] = (float) ((int *) data)[off + ix];
                                k++;
                        }
                        break;
                case GatanDM4::DataType::UNSIGNED_INT32_DATA:
                        for (int ix = x0; ix < xlast; ix++) {
                                rdata[k] = (float) ((unsigned int *) data)[off + ix];
                                k++;
                        }
                        break;
                case GatanDM4::DataType::REAL4_DATA:
                        for (int ix = x0; ix < xlast; ix++) {
                                rdata[k] = (float) ((float *) data)[off + ix];
                                k++;
                        }
                        break;
                case GatanDM4::DataType::REAL8_DATA:
                        for (int ix = x0; ix < xlast; ix++) {
                                rdata[k] = (float) ((double *) data)[off + ix];
                                k++;
                        }
                        break;                          
                default:
                        string desc = string("unsupported DM4 data type") +
                                string(GatanDM4::to_str((GatanDM4::DataType::GatanDataType) data_type));
                        throw ImageReadException(filename, desc);
                        k += xlen;
                }
        }
 
// #include "debug_read_data.h"
 
        EXITFUNC;
        return 0;
 
        EXITFUNC;
}
 
bool DM4IO::is_complex_mode()
{
        return false;
}
 
int DM4IO::write_header(const Dict &, int, const Region* , EMUtil::EMDataType, bool)
{
        ENTERFUNC;
        LOGWARN("DM4 write is not supported.");
        EXITFUNC;
        return 1;
}
 
int DM4IO::write_data(float *, int, const Region* , EMUtil::EMDataType, bool)
{
        ENTERFUNC;
        LOGWARN("DM4 write is not supported.");
        EXITFUNC;
        return 1;
}
 
int DM4IO::get_nimg()
{
        init();
 
        TagGroup root_group(file, tagtable, "");
        root_group.read_tag_group(true, 0, 1);
 
        return tagtable->get_image_counted();
}
 
void DM4IO::flush()
{
}
 
int GatanDM4::to_em_datatype(int gatan_datatype)
{
        DataType::GatanDataType type = static_cast < DataType::GatanDataType > (gatan_datatype);
        int t = 0;
 
        switch (type) {
        case GatanDM4::DataType::SIGNED_INT8_DATA:
                t = EMUtil::EM_CHAR;
                break;
        case GatanDM4::DataType::UNSIGNED_INT8_DATA:
                t = EMUtil::EM_UCHAR;
                break;
        case GatanDM4::DataType::SIGNED_INT16_DATA:
                t = EMUtil::EM_SHORT;
                break;
        case GatanDM4::DataType::UNSIGNED_INT16_DATA:
                t = EMUtil::EM_USHORT;
                break;
        case GatanDM4::DataType::SIGNED_INT32_DATA:
                t = EMUtil::EM_INT;
                break;
        case GatanDM4::DataType::UNSIGNED_INT32_DATA:
                t = EMUtil::EM_UINT;
                break;
        default:
                t = EMUtil::EM_UNKNOWN;
        }
 
        return t;
}
 
 
const char *GatanDM4::to_str(TagData::Type type)
{
        const char *str = "unknown";
 
        switch (type) {
        case TagData::SHORT:
                str = "short";
                break;
        case TagData::INT:
                str = "int";
                break;
        case TagData::USHORT:
                str = "unsigned short";
                break;
        case TagData::UINT:
                str = "unsigned int";
                break;
        case TagData::FLOAT:
                str = "float";
                break;
        case TagData::DOUBLE:
                str = "double";
                break;
        case TagData::BOOLEAN:
                str = "boolean";
                break;
        case TagData::CHAR:
                str = "char";
                break;
        case TagData::OCTET:
                str = "octet";
                break;
        case TagData::STRUCT:
                str = "struct";
                break;
        case TagData::STRING:
                str = "string";
                break;
        case TagData::ARRAY:
                str = "array";
                break;
        default:
                str = "unknown";
        }
        return str;
}
 
const char *GatanDM4::to_str(TagEntry::EntryType type)
{
        const char *str = "unknown";
 
        switch (type) {
        case TagEntry::GROUP_TAG:
                str = "Group";
                break;
        case TagEntry::DATA_TAG:
                str = "Data";
                break;
        default:
                str = "unknown";
        }
        return str;
}
 
 
const char *GatanDM4::to_str(GatanDM4::DataType::GatanDataType type)
{
        switch (type) {
        case GatanDM4::DataType::SIGNED_INT16_DATA:
                return "SIGNED_INT16_DATA";
        case GatanDM4::DataType::REAL4_DATA:
                return "REAL4_DATA";
        case GatanDM4::DataType::COMPLEX8_DATA:
                return "COMPLEX8_DATA";
        case GatanDM4::DataType::OBSELETE_DATA:
                return "OBSELETE_DATA";
        case GatanDM4::DataType::PACKED_DATA:
                return "PACKED_DATA";
        case GatanDM4::DataType::UNSIGNED_INT8_DATA:
                return "UNSIGNED_INT8_DATA";
        case GatanDM4::DataType::SIGNED_INT32_DATA:
                return "SIGNED_INT32_DATA";
        case GatanDM4::DataType::RGB_DATA:
                return "RGB_DATA";
        case GatanDM4::DataType::SIGNED_INT8_DATA:
                return "SIGNED_INT8_DATA";
        case GatanDM4::DataType::UNSIGNED_INT16_DATA:
                return "UNSIGNED_INT16_DATA";
        case GatanDM4::DataType::UNSIGNED_INT32_DATA:
                return "UNSIGNED_INT32_DATA";
        case GatanDM4::DataType::REAL8_DATA:
                return "REAL8_DATA";
        case GatanDM4::DataType::COMPLEX16_DATA:
                return "COMPLEX16_DATA";
        case GatanDM4::DataType::BINARY_DATA:
                return "BINARY_DATA";
        case GatanDM4::DataType::RGB_UINT8_0_DATA:
                return "RGB_UINT8_0_DATA";
        case GatanDM4::DataType::RGB_UINT8_1_DATA:
                return "RGB_UINT8_1_DATA";
        case GatanDM4::DataType::RGB_UINT16_DATA:
                return "RGB_UINT16_DATA";
        case GatanDM4::DataType::RGB_FLOAT32_DATA:
                return "RGB_FLOAT32_DATA";
        case GatanDM4::DataType::RGB_FLOAT64_DATA:
                return "RGB_FLOAT64_DATA";
        case GatanDM4::DataType::RGBA_UINT8_0_DATA:
                return "RGBA_UINT8_0_DATA";
        case GatanDM4::DataType::RGBA_UINT8_1_DATA:
                return "RGBA_UINT8_1_DATA";
        case GatanDM4::DataType::RGBA_UINT8_2_DATA:
                return "RGBA_UINT8_2_DATA";
        case GatanDM4::DataType::RGBA_UINT8_3_DATA:
                return "RGBA_UINT8_3_DATA";
        case GatanDM4::DataType::RGBA_UINT16_DATA:
                return "RGBA_UINT16_DATA";
        case GatanDM4::DataType::RGBA_FLOAT32_DATA:
                return "RGBA_FLOAT32_DATA";
        case GatanDM4::DataType::RGBA_FLOAT64_DATA:
                return "RGBA_FLOAT64_DATA";
        case GatanDM4::DataType::POINT2_SINT16_0_DATA:
                return "POINT2_SINT16_0_DATA";
        case GatanDM4::DataType::POINT2_SINT16_1_DATA:
                return "POINT2_SINT16_1_DATA";
        case GatanDM4::DataType::POINT2_SINT32_0_DATA:
                return "POINT2_SINT32_0_DATA";
        case GatanDM4::DataType::POINT2_FLOAT32_0_DATA:
                return "POINT2_FLOAT32_0_DATA";
        case GatanDM4::DataType::RECT_SINT16_1_DATA:
                return "RECT_SINT16_1_DATA";
        case GatanDM4::DataType::RECT_SINT32_1_DATA:
                return "RECT_SINT32_1_DATA";
        case GatanDM4::DataType::RECT_FLOAT32_1_DATA:
                return "RECT_FLOAT32_1_DATA";
        case GatanDM4::DataType::RECT_FLOAT32_0_DATA:
                return "RECT_FLOAT32_0_DATA";
        case GatanDM4::DataType::SIGNED_INT64_DATA:
                return "SIGNED_INT64_DATA";
        case GatanDM4::DataType::UNSIGNED_INT64_DATA:
                return "UNSIGNED_INT64_DATA";
        default:
                break;
        }
        return "Unknown Type";
}