void EMHeader::generate_common_header(DensityHeader &header) {
header.Objectpixelsize_ = Objectpixelsize;
header.update_map_dimensions(nx, ny, nz);
header.magic = magic;
header.set_data_type(type);
for (short i = 0; i < DensityHeader::COMMENT_FIELD_SINGLE_SIZE; i++) {
header.comments[0][i] = comment[i];
}
header.voltage = voltage;
header.Cs = Cs;
header.Aperture = Aperture;
header.Magnification = Magnification;
header.Postmagnification = Postmagnification;
header.Exposuretime = Exposuretime;
header.Microscope = Microscope;
header.Pixelsize = Pixelsize;
header.CCDArea = CCDArea;
header.Defocus = Defocus;
header.Astigmatism = Astigmatism;
header.AstigmatismAngle = AstigmatismAngle;
header.FocusIncrement = FocusIncrement;
header.CountsPerElectron = CountsPerElectron;
header.Intensity = Intensity;
header.EnergySlitwidth = EnergySlitwidth;
header.EnergyOffset = EnergyOffset;
header.Tiltangle = Tiltangle;
header.Tiltaxis = Tiltaxis;
header.MarkerX = MarkerX;
MarkerY = header.MarkerY;
header.lswap = lswap;
}
IMPEM_BEGIN_INTERNAL_NAMESPACE
EMHeader::EMHeader(const DensityHeader &header) {
nx = header.get_nx();
ny = header.get_ny();
nz = header.get_nz();
magic = header.magic;
type = header.get_data_type();
for (short i = 0; i < DensityHeader::COMMENT_FIELD_SINGLE_SIZE; i++) {
comment[i] = header.comments[0][i];
}
voltage = header.voltage;
Cs = header.Cs;
Aperture = header.Aperture;
Magnification = header.Magnification;
Postmagnification = header.Postmagnification;
Exposuretime = header.Exposuretime;
Objectpixelsize = header.get_spacing();
Microscope = header.Microscope;
Pixelsize = header.Pixelsize;
CCDArea = header.CCDArea;
Defocus = header.Defocus;
Astigmatism = header.Astigmatism;
AstigmatismAngle = header.AstigmatismAngle;
FocusIncrement = header.FocusIncrement;
CountsPerElectron = header.CountsPerElectron;
Intensity = header.Intensity;
EnergySlitwidth = header.EnergySlitwidth;
EnergyOffset = header.EnergyOffset;
Tiltangle = header.Tiltangle;
Tiltaxis = header.Tiltaxis;
MarkerX = header.MarkerX;
MarkerY = header.MarkerY;
lswap = header.lswap;
}
IMPEM_BEGIN_INTERNAL_NAMESPACE
void MRCHeader::FromDensityHeader(const DensityHeader &h)
{
std::string empty;
nz=h.get_nz(); ny=h.get_ny(); nx=h.get_nx(); // map size
// mode
if(h.get_data_type()==0) // data type not initialized
mode = 2;
if(h.get_data_type()==1)
mode=0; // 8-bits
else if(h.get_data_type()==2)
mode=1;// 16-bits
else if(h.get_data_type()==5)
mode=2;// 32-bits
// number of first columns in map (default = 0)
nxstart=h.nxstart ; nystart=h.nystart ; nzstart=h.nzstart;
mx=h.mx ; my=h.my ; mz=h.mz; // Number of intervals along each dimension
xlen=h.xlen ; ylen=h.ylen ; zlen=h.zlen; // Cell dimensions (angstroms)
alpha=h.alpha ; beta=h.beta ; gamma=h.gamma; // Cell angles (degrees)
/* Axes corresponding to columns (mapc), rows (mapr) and sections (maps)
(1,2,3 for x,y,z) */
mapc=h.mapc;
mapr=h.mapr;
maps=h.maps;
/* Minimum, maximum and mean density value */
dmin=h.dmin;
dmax=h.dmax;
dmean=h.dmean;
ispg=h.ispg; // Sapce group number 0 or 1 (default 0)
nsymbt=h.nsymbt; // Number of bytes used for symmetry data (0 or 80)
// extra space used for anything - 0 by default
for(int i=0;i<IMP_MRC_USER;i++)
user[i]=h.user[i];
strcpy(map,"MAP\0"); // character string 'MAP ' to identify file type
// Origin used for transforms
xorigin=h.get_xorigin() ; yorigin=h.get_yorigin() ; zorigin=h.get_zorigin();
// machine stamp (0x11110000 bigendian, 0x44440000 little)
machinestamp=h.machinestamp;
rms=h.rms; // RMS deviation of map from mean density
nlabl=h.nlabl; // Number of labels being used
// Copy comments
for(int i=0;i<nlabl;i++)
strcpy(labels[i],h.comments[i]);
// Fill empty coments with null character
const char *c="\0";
empty.resize(IMP_MRC_LABEL_SIZE,*c);
for(int i=nlabl;i<IMP_MRC_NUM_LABELS;i++)
strcpy(labels[i],empty.c_str());
}
//! Function to transfer the (compatible) information content from DensityHeader
//! to ImageHeader
void DensityHeader_to_ImageHeader(const DensityHeader& dh,ImageHeader& h) {
// map size
h.set_number_of_slices(dh.get_nz());
h.set_number_of_rows(dh.get_ny());
h.set_number_of_columns(dh.get_nx());
// mode
switch (dh.get_data_type()) {
case 1:
h.set_image_type(ImageHeader::VOL_BYTE);
break;
case 2:
h.set_image_type(ImageHeader::VOL_INT);
break;
case 5:
h.set_image_type(ImageHeader::VOL_IMPEM);
break;
}
// Reversed image?
if(algebra::get_is_big_endian()) {
h.set_reversed(dh.lswap!=1);
} else {
h.set_reversed(dh.lswap==1);
}
// Origins and pixel size
h.set_origin(algebra::Vector3D(dh.get_xorigin(),
dh.get_yorigin(),
dh.get_zorigin()) );
h.set_object_pixel_size(dh.get_spacing());
// Statistical values. There is no field in DensityHeader to guarantee that
// they are computed or correct, so they are ignored
h.set_fImami(0.);
h.set_fFmax(0.);
h.set_fFmin(0.);
h.set_fAv(0.);
h.set_fSig(0.);
// These fields don't have an equivalent in DensityHeader
h.set_Scale(1.);
h.set_fAngle1(0.);
h.set_Weight(1.);
h.set_Flip(0.);
h.set_fNrec(0.);
h.set_fNlabel(0.);
h.set_fIhist(0.);
h.set_fLabrec(0.);
h.set_fIangle(0.);
h.set_fLabbyt(0.);
h.set_fLenbyt(0.);
h.set_fFlag(0.); // Ignore all the Euler angles for the Spider Image
// Set time and date
h.set_date();
h.set_time();
}
IMPEM_BEGIN_NAMESPACE
void MRCReaderWriter::read(const char *fn_in, float **data, DensityHeader &head)
{
// Read file
filename.assign(fn_in);
read(data);
// Translate header to DensityHeader
header.ToDensityHeader(head);
head.Objectpixelsize_ = (float)head.xlen/head.get_nx();
}
void MRCHeader::ToDensityHeader(DensityHeader &h)
{
std::string empty;
h.update_map_dimensions(nx,ny,nz);
h.update_cell_dimensions();
// mode
if(mode==0)
h.set_data_type(1);
else if(mode==1)
h.set_data_type(2);
else if(mode==2)
h.set_data_type(5);
// number of first columns in map (default = 0)
h.nxstart=nxstart ; h.nystart=nystart ; h.nzstart=nzstart;
h.mx=mx ; h.my=my ; h.mz=mz; // Number of intervals along each dimension
h.xlen=xlen;h.ylen=ylen;h.zlen=zlen;//Cell dimentions(amgstroms)
h.alpha=alpha ; h.beta=beta ; h.gamma=gamma; // Cell angles (degrees)
/* Axes corresponding to columns (mapc), rows (mapr) and sections (maps)
(1,2,3 for x,y,z) */
h.mapc=mapc;
h.mapr=mapr;
h.maps=maps;
/* Minimum, maximum and mean density value */
h.dmin=dmin;
h.dmax=dmax;
h.dmean=dmean;
h.ispg=ispg; // Sapce group number 0 or 1 (default 0)
h.nsymbt=nsymbt; // Number of bytes used for symmetry data (0 or 80)
// extra space used for anything - 0 by default
for(int i=0;i<IMP_MRC_USER;i++)
h.user[i]=user[i];
strcpy(h.map,"MAP\0"); // character string 'MAP ' to identify file type
// Origin used for transforms
h.set_xorigin(xorigin) ; h.set_yorigin(yorigin) ; h.set_zorigin(zorigin);
// machine stamp (0x11110000 bigendian, 0x44440000 little)
h.machinestamp=machinestamp;
h.rms=rms; // RMS deviation of map from mean density
h.nlabl=nlabl; // Number of labels being used
// Copy comments
for(int i=0;i<h.nlabl;i++) {
//to make sure there is not memory leak
std::string temp;
temp.copy(labels[i],DensityHeader::COMMENT_FIELD_SINGLE_SIZE,0);
strcpy(h.comments[i],temp.c_str());
}
// Fill empty coments with null character
const char *c="\0";
empty.resize(IMP_MRC_LABEL_SIZE,*c);
for(int i=h.nlabl;i<IMP_MRC_NUM_LABELS;i++)
strcpy(h.comments[i],empty.c_str());
}
DensityHeader create_density_header(const algebra::BoundingBoxD<3> &bb,
float spacing) {
DensityHeader header;
algebra::Vector3D origin=bb.get_corner(0);
algebra::Vector3D top=bb.get_corner(1);
header.set_xorigin(origin[0]);
header.set_yorigin(origin[1]);
header.set_zorigin(origin[2]);
header.Objectpixelsize_=spacing;
//calculate the extent of the map
int extent[3];
for(int i=0;i<3;i++) {
extent[i]=ceil((top[i]-origin[i])/spacing);
}
header.update_map_dimensions(extent[0],extent[1],extent[2]);
header.compute_xyz_top(true);
return header;
}
IMPEM_BEGIN_NAMESPACE
//! Function to transfer the (compatible) information content from ImageHeader
//! to DensityHeader
void ImageHeader_to_DensityHeader(const ImageHeader &h, DensityHeader &dh) {
std::string empty;
// map size and voxel size
dh.update_map_dimensions(static_cast<int>(h.get_number_of_columns()),
static_cast<int>(h.get_number_of_rows()),
static_cast<int>(h.get_number_of_slices()));
dh.Objectpixelsize_ = h.get_object_pixel_size();
// mode
switch ((int)h.get_fIform()) {
case ImageHeader::IMG_BYTE:
dh.set_data_type(1);
break;
case ImageHeader::IMG_IMPEM:
dh.set_data_type(5);
break;
case ImageHeader::IMG_INT:
dh.set_data_type(2);
break;
case ImageHeader::VOL_BYTE:
dh.set_data_type(1);
break;
case ImageHeader::VOL_IMPEM:
dh.set_data_type(5);
break;
case ImageHeader::VOL_INT:
dh.set_data_type(2);
break;
}
// number of first columns in map (default = 0)
dh.nxstart = 0;
dh.nystart = 0;
dh.nzstart = 0;
// Number of intervals along each dimension. In DensityHeader it is assumed
// to be equal to the size of the map
dh.mx = dh.get_nx();
dh.my = dh.get_ny();
dh.mz = dh.get_nz();
// Cell angles (degrees)
// Spider format does not have these fields. Filed with default (90 deg)
dh.alpha = 90.;
dh.beta = 90.;
dh.gamma = 90.;
/* Axes corresponding to columns (mapc), rows (mapr) and slices (maps)
They are given the default values (1,2,3 for x,y,z) */
dh.mapc = 1;
dh.mapr = 2;
dh.maps = 3;
// Statistical values: Minimum, maximum, mean, standard deviation
// Only set them if computed
if ((int)h.get_fImami() == 1) {
dh.dmin = h.get_fFmin();
dh.dmax = h.get_fFmax();
dh.dmean = h.get_fAv();
dh.rms = h.get_fSig();
} else {
dh.dmin = 0;
dh.dmax = 0;
dh.dmean = 0;
dh.rms = 0;
}
dh.ispg = 0; // Sapce group number 0 or 1 (default 0)
dh.nsymbt = 0; // Number of bytes used for symmetry data (0 or 80, default 0)
std::strcpy(dh.map, "MAP\0"); // string 'MAP ' to identify file type
// Origin used for transforms
algebra::Vector3D origin = h.get_origin();
dh.set_xorigin(origin[0]);
dh.set_yorigin(origin[1]);
dh.set_zorigin(origin[2]);
/* CCP4 convention machine stamp: 0x11110000 for big endian, or
0x44440000 for little endian */
unsigned char *ch;
ch = (unsigned char *)&dh.machinestamp;
if (algebra::get_is_big_endian()) {
ch[0] = ch[1] = 0x11;
ch[2] = ch[3] = 0;
} else {
ch[0] = ch[1] = 0x44;
ch[2] = ch[3] = 0;
}
// Number of labels being used (default, 0)
dh.nlabl = 0;
// Reversed image or not
if (h.get_reversed() == true) {
if (algebra::get_is_big_endian()) {
dh.lswap = 0;
} else {
dh.lswap = 1;
}
} else {
if (algebra::get_is_big_endian()) {
dh.lswap = 1;
} else {
dh.lswap = 0;
}
}
}
