void EMData::read_image(const string & filename, int img_index, bool nodata,
const Region * region, bool is_3d)
{
ENTERFUNC;
ImageIO *imageio = EMUtil::get_imageio(filename, ImageIO::READ_ONLY);
if (!imageio) {
throw ImageFormatException("cannot create an image io");
}
else {
int err = imageio->read_header(attr_dict, img_index, region, is_3d);
if (err) {
throw ImageReadException(filename, "imageio read header failed");
}
else {
LstIO * myLstIO = dynamic_cast<LstIO *>(imageio);
if(!myLstIO) attr_dict["source_path"] = filename; //"source_path" is set to full path of reference image for LstIO, so skip this statement
attr_dict["source_n"] = img_index;
if (imageio->is_complex_mode()) {
set_complex(true);
set_fftpad(true);
}
if (attr_dict.has_key("is_fftodd") && (int)attr_dict["is_fftodd"] == 1) {
set_fftodd(true);
}
if ((int) attr_dict["is_complex_ri"] == 1) {
set_ri(true);
}
save_byteorder_to_dict(imageio);
nx = attr_dict["nx"];
ny = attr_dict["ny"];
nz = attr_dict["nz"];
attr_dict.erase("nx");
attr_dict.erase("ny");
attr_dict.erase("nz");
if (!nodata) {
if (region) {
nx = (int)region->get_width();
if (nx <= 0) nx = 1;
ny = (int)region->get_height();
if (ny <= 0) ny = 1;
nz = (int)region->get_depth();
if (nz <= 0) nz = 1;
set_size(nx,ny,nz);
to_zero(); // This could be avoided in favor of setting only the regions that were not read to to zero... but tedious
} // else the dimensions of the file being read match those of this
else {
set_size(nx, ny, nz);
}
// If GPU features are enabled there is danger that rdata will
// not be allocated, but set_size takes care of this, so this
// should be safe.
int err = imageio->read_data(get_data(), img_index, region, is_3d);
if (err) {
throw ImageReadException(filename, "imageio read data failed");
}
else {
update();
}
}
else {
if (rdata!=0) EMUtil::em_free(rdata);
rdata=0;
}
}
}
#ifndef IMAGEIO_CACHE
if( imageio )
{
#ifdef HDFIO_CACHE
if(dynamic_cast<HdfIO2*>(imageio)==NULL && dynamic_cast<HdfIO*>(imageio)==NULL) {
#endif //HDFIO_CACHE
delete imageio;
imageio = 0;
#ifdef HDFIO_CACHE
}
#endif //HDFIO_CACHE
}
#endif //IMAGEIO_CACHE
EXITFUNC;
}
void EMData::read_binedimage(const string & filename, int img_index, int binfactor, bool fast, bool is_3d)
{
ENTERFUNC;
ImageIO *imageio = EMUtil::get_imageio(filename, ImageIO::READ_ONLY);
if (!imageio) {
throw ImageFormatException("cannot create an image io");
}
else {
int err = imageio->read_header(attr_dict, img_index, 0, is_3d);
if (err) {
throw ImageReadException(filename, "imageio read header failed");
}
else {
attr_dict["source_path"] = filename;
attr_dict["source_n"] = img_index;
if (imageio->is_complex_mode()) {
set_complex(true);
set_fftpad(true);
}
if (attr_dict.has_key("is_fftodd") && (int)attr_dict["is_fftodd"] == 1) {
set_fftodd(true);
}
if ((int) attr_dict["is_complex_ri"] == 1) {
set_ri(true);
}
save_byteorder_to_dict(imageio);
int ori_nx = nx = attr_dict["nx"];
int ori_ny = ny = attr_dict["ny"];
int ori_nz = nz = attr_dict["nz"];
attr_dict.erase("nx");
attr_dict.erase("ny");
attr_dict.erase("nz");
// At this point nx, ny and nz are all reduced by binfactor
set_size(nx/binfactor, ny/binfactor, nz/binfactor);
//here is where we read in the binned data
EMData* tempdata = new EMData();
size_t sizeofslice = nx*ny*sizeof(float);
//zbin factor use 1 to speed binning(but don't benfit by averaging in Z)
int zbin = binfactor;
if(fast) zbin = 1;
//verbose
float percent = 0.1f;
for(int k = 0; k < ori_nz; k+=binfactor){
if(k > ori_nz*percent){
cout << float(k)/float(ori_nz) << "% Done!" << endl;
percent+=0.1f;
}
// read in a slice region
const Region* binregion = new Region(0,0,k,ori_nx,ori_ny,zbin);
tempdata->read_image(filename, 0, false, binregion);
// shrink the slice
if (binfactor > 1) tempdata->process_inplace("math.meanshrink",Dict("n",binfactor));
size_t offset = nx*ny*k/binfactor;
//add slice to total
EMUtil::em_memcpy(get_data()+offset,tempdata->get_data(),sizeofslice);
delete binregion;
}
delete tempdata;
update();
}
}
#ifndef IMAGEIO_CACHE
if( imageio )
{
#ifdef HDFIO_CACHE
if(dynamic_cast<HdfIO2*>(imageio)==NULL && dynamic_cast<HdfIO*>(imageio)==NULL) {
#endif //HDFIO_CACHE
delete imageio;
imageio = 0;
#ifdef HDFIO_CACHE
}
#endif //HDFIO_CACHE
}
#endif //IMAGEIO_CACHE
EXITFUNC;
}