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;
}
void EMUtil::getRenderLimits(const Dict & dict, float & rendermin, float & rendermax)
{
const char min_or_max_flag = 'm';
const char std_devs_flag = 's';
const float flag_base = 1.0e30;
const float use_data_min_or_max = -flag_base;
string svalue;
const char * str;
char flag;
float num_std_devs;
bool debug = (getenv("DEBUG_RENDER_LIMITS") != NULL);
rendermin = 0.0;
rendermax = 0.0;
if (debug) {
printf ("into RenderLimits, rmin = %g, rmax = %g\n", rendermin, rendermax);
}
if (dict.has_key("render_min")) {
svalue = static_cast<string>(dict["render_min"]);
str = svalue.c_str();
flag = str[0];
if (debug) printf ("render_min = %s\n", str);
if (flag == min_or_max_flag) {
rendermin = use_data_min_or_max;
}
else if (flag == std_devs_flag) {
num_std_devs = 4.0;
sscanf (str+1, "%g", & num_std_devs);
rendermin = flag_base * num_std_devs;
}
else {
rendermin = (float) dict["render_min"];
}
}
if (dict.has_key("render_max")) {
svalue = static_cast<string>(dict["render_max"]);
str = svalue.c_str();
flag = str[0];
if (debug) printf ("render_max = %s\n", str);
if (flag == min_or_max_flag) {
rendermax = use_data_min_or_max;
}
else if (flag == std_devs_flag) {
num_std_devs = 4.0;
sscanf (str+1, "%g", & num_std_devs);
rendermax = flag_base * num_std_devs;
}
else {
rendermax = (float) dict["render_max"];
}
}
if (debug) {
printf ("out of RenderLimits, rmin = %g, rmax = %g\n", rendermin, rendermax);
}
}
int PgmIO::write_header(const Dict & dict, int image_index, const Region*,
EMUtil::EMDataType, bool)
{
ENTERFUNC;
int err = 0;
//single image format, index can only be zero
if(image_index == -1) {
image_index = 0;
}
if(image_index != 0) {
throw ImageWriteException(filename, "PGM file does not support stack.");
}
check_write_access(rw_mode, image_index);
int nz = dict["nz"];
if ((int)nz != 1) {
LOGERR("Cannot write 3D image as PGM. Your image nz = %d", nz);
err = 1;
throw ImageWriteException("N/A", "Cannot write 3D image as PGM.");
}
else {
nx = dict["nx"];
ny = dict["ny"];
if(dict.has_key("min_grey")) minval = dict["min_gray"];
if(dict.has_key("max_grey")) maxval = dict["max_gray"];
//if we didn't get any good values from attributes, assign to 255 by default
#ifdef _WIN32
if (maxval<=minval || _isnan(minval) || _isnan(maxval)) {
#else
if (maxval<=minval || std::isnan(minval) || std::isnan(maxval)) {
#endif //_WIN32
maxval = 255;
}
if(dict.has_key("render_min")) rendermin=(float)dict["render_min"]; // float value representing black in the output
if(dict.has_key("render_max")) rendermax=(float)dict["render_max"]; // float value representign white in the output
fprintf(pgm_file, "%s\n%d %d\n%d\n", MAGIC_BINARY, nx, ny, maxval);
}
EXITFUNC;
return err;
}
int PgmIO::read_data(float *data, int image_index, const Region * area, bool)
{
ENTERFUNC;
//single image format, index can only be zero
image_index = 0;
check_read_access(image_index, data);
check_region(area, IntSize(nx, ny));
portable_fseek(pgm_file, file_offset, SEEK_SET);
unsigned char *cdata = (unsigned char *) (data);
size_t mode_size = sizeof(unsigned char);
EMUtil::process_region_io(cdata, pgm_file, READ_ONLY, image_index,
mode_size, nx, ny, 1, area, true);
int xlen = 0, ylen = 0;
EMUtil::get_region_dims(area, nx, &xlen, ny, &ylen);
for (int k = xlen * ylen - 1; k >= 0; k--) {
data[k] = static_cast < float >(cdata[k]);
}
EXITFUNC;
return 0;
}