void readParams()
{
fn_in = getParam("-i");
fn_root = getParam("--oroot");
invert = checkParam("--invert");
min_size = getDoubleParam("--min_size");
if (fn_root == "")
fn_root = fn_in.withoutExtension();
}
void ProgXrayImport::readGeoInfo(const FileName &fn, MDRow &rowGeo) const
{
double tiltAngle;
switch (dSource)
{
case MISTRAL:
tiltAngle = dMi(anglesArray, fn.getPrefixNumber()-1);
break;
case BESSY:
case GENERIC:
{
FileName fnBase = fn.withoutExtension();
std::ifstream fhPosition;
fhPosition.open((fnBase+"-positions.txt").c_str());
if (!fhPosition)
REPORT_ERROR(ERR_IO_NOTEXIST,fnBase+"-positions.txt");
int itemsFound=0;
std::string line;
std::vector<std::string> tokens;
while (!fhPosition.eof())
{
getline(fhPosition,line);
splitString(line," ",tokens);
if (tokens[0]=="xm:sample:rx")
{
tiltAngle=textToFloat(tokens[1]);
itemsFound++;
}
if (itemsFound==1)
break;
}
fhPosition.close();
if (itemsFound!=1)
REPORT_ERROR(ERR_VALUE_EMPTY,(std::string)"Cannot find tilt angle in "+
fnBase+"-positions.txt");
}
break;
}
rowGeo.setValue(MDL_ANGLE_TILT, tiltAngle);
}
void ProgXrayImport::readCorrectionInfo(const FileName &fn, double ¤tBeam,
double &expTime, double &slitWidth) const
{
FileName fnBase = fn.withoutExtension();
std::ifstream fhPosition;
fhPosition.open((fnBase+"-positions.txt").c_str());
if (!fhPosition)
REPORT_ERROR(ERR_IO_NOTEXIST,fnBase+"-positions.txt");
int itemsFound = 0;
std::string line;
std::vector<std::string> tokens;
while (!fhPosition.eof())
{
getline(fhPosition,line);
splitString(line," ",tokens);
if (tokens[0]=="sr:current")
{
currentBeam = textToFloat(tokens[1]);
itemsFound++;
}
else if (tokens[0]=="xm:ccd:exp_time")
{
expTime = textToFloat(tokens[1]);
itemsFound++;
}
else if (tokens[0]=="xm:mono:slitwidth")
{
slitWidth = textToFloat(tokens[1]);
itemsFound++;
}
if (itemsFound==3)
break;
}
fhPosition.close();
if ( itemsFound != 3 )
REPORT_ERROR(ERR_VALUE_EMPTY,(std::string)"Cannot find all parameters in "+
fnBase+"-positions.txt");
}
void run()
{
// First do a crude search over the given parameter optimization space
// Optimize the number of pairs here...
int npart = optimiseTransformationMatrix(true);
// Get rid of double pairs (two different untilted coordinates are close to a tilted coordinate)
int nprune = 0;
nprune = prunePairs(best_x, best_y);
// Calculate average distance between the pairs
double avgdist = getAverageDistance(best_x, best_y);
std::cout << " Before optimization of the passing matrix: "<<std::endl;
std::cout << " - Number of pruned pairs= "<<nprune<<std::endl;
std::cout << " - best_rot= " << best_rot << " best_tilt= " << best_tilt << " best_x= " << best_x << " best_y= " << best_y << std::endl;
std::cout << " - Number of particle pairs= " << npart << " average distance= " <<avgdist<<std::endl;
#define WRITE_MAPPED
#ifdef WRITE_MAPPED
std::ofstream fh;
FileName fn_map;
fn_map = "mapped.box";
fh.open(fn_map.c_str(), std::ios::out);
for (int i = 0; i < p_map.size()/2; i++)
{
fh << p_map[2*i] + best_x -dim/2<< " " << p_map[2*i+1] + best_y -dim/2<< " "<<dim<<" "<<dim<<" -3"<<std::endl;
//if (pairs[i]>=0)
// std::cerr << " i= " << i << " pairs[i]= " << pairs[i] << std::endl;
}
fh.close();
#endif
if (do_opt)
{
optimiseTransformationMatrixContinuous();
npart = getNumberOfPairs();
nprune = prunePairs();
avgdist = getAverageDistance();
std::cout << " After optimization of the passing matrix: "<<std::endl;
std::cout << " - Number of pruned pairs= "<<nprune<<std::endl;
std::cout << " - Final number of particle pairs= " << npart << " average distance= " <<avgdist<<std::endl;
}
#ifdef WRITE_MAPPED
fn_map = "mapped_opt.box";
fh.open(fn_map.c_str(), std::ios::out);
for (int i = 0; i < p_map.size()/2; i++)
{
fh << p_map[2*i] -dim/2<< " " << p_map[2*i+1] -dim/2<<" "<<dim<<" "<<dim<<" -3"<< std::endl;
}
fh.close();
#endif
// Write out STAR files with the coordinates
MetaDataTable MDu, MDt;
for (int t = 0; t < p_til.size()/2; t++)
{
int u = pairs_t2u[t];
if (u >= 0)
{
MDu.addObject();
MDu.setValue(EMDL_IMAGE_COORD_X, ((double)(p_unt[2*u])));
MDu.setValue(EMDL_IMAGE_COORD_Y, ((double)(p_unt[2*u+1])));
MDt.addObject();
MDt.setValue(EMDL_IMAGE_COORD_X, ((double)(p_til[2*t])));
MDt.setValue(EMDL_IMAGE_COORD_Y, ((double)(p_til[2*t+1])));
}
}
fn_unt = fn_unt.withoutExtension() + "_pairs.star";
fn_til = fn_til.withoutExtension() + "_pairs.star";
MDu.write(fn_unt);
MDt.write(fn_til);
std::cout << " Written out coordinate STAR files: " << fn_unt << " and " << fn_til <<std::endl;
std::cout << " Done!" << std::endl;
}
