void roundShifts(MDRow &row)
{
double aux = 0.;
if (row.getValue(MDL_SHIFT_X, aux))
{
aux = (double)ROUND(aux);
row.setValue(MDL_SHIFT_X, aux);
}
if (row.getValue(MDL_SHIFT_Y, aux))
{
aux = (double)ROUND(aux);
row.setValue(MDL_SHIFT_Y, aux);
}
}
// Continuous assignment ===================================================
double ProgNmaAlignment::performContinuousAssignment(const FileName &fnRandom,
int pyramidLevel) const {
// Perform alignment
const char * randStr = fnRandom.c_str();
String fnResults=formatString("%s_anglecont.xmd", randStr);
bool costSource=true;
String program = "xmipp_angular_continuous_assign";
String arguments =
formatString(
"-i %s_angledisc.xmd --ref %s_deformedPDB.vol -o %s --gaussian_Fourier %f --gaussian_Real %f --zerofreq_weight %f -v 0",
randStr, randStr, fnResults.c_str(), gaussian_DFT_sigma,
gaussian_Real_sigma, weight_zero_freq);
runSystem(program, arguments, false);
// Pick up results
MetaData DF(fnResults);
MDRow row;
DF.getRow(row, DF.firstObject());
row.getValue(MDL_ANGLE_ROT, trial(VEC_XSIZE(trial) - 5));
row.getValue(MDL_ANGLE_TILT, trial(VEC_XSIZE(trial) - 4));
row.getValue(MDL_ANGLE_PSI, trial(VEC_XSIZE(trial) - 3));
row.getValue(MDL_SHIFT_X, trial(VEC_XSIZE(trial) - 2));
trial(VEC_XSIZE(trial) - 2) *= pow(2.0, (double) pyramidLevel);
row.getValue(MDL_SHIFT_Y, trial(VEC_XSIZE(trial) - 1));
trial(VEC_XSIZE(trial) - 1) *= pow(2.0, (double) pyramidLevel);
double tempvar;
if (!costSource) {
row.getValue(MDL_MAXCC, tempvar);
tempvar = -tempvar;
} else
row.getValue(MDL_COST, tempvar);
return tempvar;
}
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 processImage(const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut)
{
ImageGeneric img;
switch (operation)
{
case HEADER_PRINT:
img.read(fnImg, _HEADER_ALL);
img.print();
break;
case HEADER_EXTRACT:
img.read(fnImg, _HEADER_ALL);
rowOut = img.getGeometry();
if (round_shifts)
roundShifts(rowOut);
rowOut.setValue(MDL_IMAGE, fnImgOut);
break;
case HEADER_ASSIGN:
rowOut = rowIn;
if (round_shifts)
roundShifts(rowOut);
img.readApplyGeo(fnImg, rowOut, params);
img.setDataMode(_HEADER_ALL);
img.write(fnImg, ALL_IMAGES, fnImg.isInStack(), WRITE_REPLACE);
break;
case HEADER_RESET:
img.read(fnImg, _HEADER_ALL);
img.initGeometry();
img.write(fnImg, ALL_IMAGES, fnImg.isInStack(), WRITE_REPLACE);
break;
case HEADER_SAMPLINGRATE:
{
img.read(fnImg, _HEADER_ALL);
if (sampling < 0)
{
double samplingRead;
img.image->MDMainHeader.getValue(MDL_SAMPLINGRATE_X, samplingRead);
std::cout << samplingRead << std::endl;
}
else
{
img.image->MDMainHeader.setValue(MDL_SAMPLINGRATE_X, sampling);
img.image->MDMainHeader.setValue(MDL_SAMPLINGRATE_Y, sampling);
img.image->MDMainHeader.setValue(MDL_SAMPLINGRATE_Z, sampling);
img.write(fnImg, ALL_IMAGES, fnImg.isInStack(), WRITE_REPLACE);
std::cout << "New sampling rate (Angstrom) = " << sampling << std::endl;
}
}
break;
case HEADER_TREE:
{
XmippH5File H5File;
FileName filename = fnImg.removeAllPrefixes().removeFileFormat();
if (H5File.isHdf5(filename.c_str()))
{
H5File.openFile(fnImg.removeAllPrefixes().removeFileFormat(), H5F_ACC_RDONLY);
H5File.showTree();
}
else
REPORT_ERROR(ERR_IMG_UNKNOWN, "Unknown file format to display its data structure.");
}
break;
}
}
void ProgSortByStatistics::run()
{
// Process input selfile ..............................................
SF.read(fn);
SF.removeDisabled();
MetaData SF2 = SF;
SF = SF2;
bool trained = false;
if (fn_train != "")
{
SFtrain.read(fn_train);
processInprocessInputPrepareSPTH(SFtrain,trained);
trained = true;
processInprocessInputPrepareSPTH(SF,trained);
}
else
processInprocessInputPrepareSPTH(SF,trained);
int imgno = 0;
int numPCAs = pcaAnalyzer.size();
MultidimArray<double> finalZscore(SF.size());
MultidimArray<double> ZscoreShape1(SF.size()), sortedZscoreShape1;
MultidimArray<double> ZscoreShape2(SF.size()), sortedZscoreShape2;
MultidimArray<double> ZscoreSNR1(SF.size()), sortedZscoreSNR1;
MultidimArray<double> ZscoreSNR2(SF.size()), sortedZscoreSNR2;
MultidimArray<double> ZscoreHist(SF.size()), sortedZscoreHist;
finalZscore.initConstant(0);
ZscoreShape1.resizeNoCopy(finalZscore);
ZscoreShape2.resizeNoCopy(finalZscore);
ZscoreSNR1.resizeNoCopy(finalZscore);
ZscoreSNR2.resizeNoCopy(finalZscore);
ZscoreHist.resizeNoCopy(finalZscore);
sortedZscoreShape1.resizeNoCopy(finalZscore);
sortedZscoreShape2.resizeNoCopy(finalZscore);
sortedZscoreSNR1.resizeNoCopy(finalZscore);
sortedZscoreSNR2.resizeNoCopy(finalZscore);
sortedZscoreHist.resizeNoCopy(finalZscore);
double zScore=0;
int enabled;
FOR_ALL_OBJECTS_IN_METADATA(SF)
{
SF.getValue(MDL_ENABLED,enabled,__iter.objId);
if ( (enabled==-1) )
{
A1D_ELEM(finalZscore,imgno) = 1e3;
A1D_ELEM(ZscoreShape1,imgno) = 1e3;
A1D_ELEM(ZscoreShape2,imgno) = 1e3;
A1D_ELEM(ZscoreSNR1,imgno) = 1e3;
A1D_ELEM(ZscoreSNR2,imgno) = 1e3;
A1D_ELEM(ZscoreHist,imgno) = 1e3;
imgno++;
enabled = 0;
}
else
{
for (int num = 0; num < numPCAs; ++num)
{
if (num == 0)
{
A1D_ELEM(ZscoreSNR1,imgno) = pcaAnalyzer[num].getZscore(imgno);
}
else if (num == 1)
{
A1D_ELEM(ZscoreShape2,imgno) = pcaAnalyzer[num].getZscore(imgno);
}
else if (num == 2)
{
A1D_ELEM(ZscoreShape1,imgno) = pcaAnalyzer[num].getZscore(imgno);
}
else if (num == 3)
{
A1D_ELEM(ZscoreSNR2,imgno) = pcaAnalyzer[num].getZscore(imgno);
}
else
{
A1D_ELEM(ZscoreHist,imgno) = pcaAnalyzer[num].getZscore(imgno);
}
if(zScore < pcaAnalyzer[num].getZscore(imgno))
zScore = pcaAnalyzer[num].getZscore(imgno);
}
A1D_ELEM(finalZscore,imgno)=zScore;
imgno++;
zScore = 0;
}
}
pcaAnalyzer.clear();
// Produce output .....................................................
MetaData SFout;
std::ofstream fh_zind;
if (verbose==2 && !fn_out.empty())
fh_zind.open((fn_out.withoutExtension() + "_vectors.xmd").c_str(), std::ios::out);
MultidimArray<int> sorted;
finalZscore.indexSort(sorted);
int nr_imgs = SF.size();
bool thereIsEnable=SF.containsLabel(MDL_ENABLED);
MDRow row;
for (int imgno = 0; imgno < nr_imgs; imgno++)
{
int isort_1 = DIRECT_A1D_ELEM(sorted,imgno);
int isort = isort_1 - 1;
SF.getRow(row, isort_1);
if (thereIsEnable)
{
int enabled;
row.getValue(MDL_ENABLED, enabled);
if (enabled==-1)
continue;
}
double zscore=DIRECT_A1D_ELEM(finalZscore,isort);
double zscoreShape1=DIRECT_A1D_ELEM(ZscoreShape1,isort);
double zscoreShape2=DIRECT_A1D_ELEM(ZscoreShape2,isort);
double zscoreSNR1=DIRECT_A1D_ELEM(ZscoreSNR1,isort);
double zscoreSNR2=DIRECT_A1D_ELEM(ZscoreSNR2,isort);
double zscoreHist=DIRECT_A1D_ELEM(ZscoreHist,isort);
DIRECT_A1D_ELEM(sortedZscoreShape1,imgno)=DIRECT_A1D_ELEM(ZscoreShape1,isort);
DIRECT_A1D_ELEM(sortedZscoreShape2,imgno)=DIRECT_A1D_ELEM(ZscoreShape2,isort);
DIRECT_A1D_ELEM(sortedZscoreSNR1,imgno)=DIRECT_A1D_ELEM(ZscoreSNR1,isort);
DIRECT_A1D_ELEM(sortedZscoreSNR2,imgno)=DIRECT_A1D_ELEM(ZscoreSNR2,isort);
DIRECT_A1D_ELEM(sortedZscoreHist,imgno)=DIRECT_A1D_ELEM(ZscoreHist,isort);
if (zscore>cutoff && cutoff>0)
{
row.setValue(MDL_ENABLED,-1);
if (addToInput)
SF.setValue(MDL_ENABLED,-1,isort_1);
}
else
{
row.setValue(MDL_ENABLED,1);
if (addToInput)
SF.setValue(MDL_ENABLED,1,isort_1);
}
row.setValue(MDL_ZSCORE,zscore);
row.setValue(MDL_ZSCORE_SHAPE1,zscoreShape1);
row.setValue(MDL_ZSCORE_SHAPE2,zscoreShape2);
row.setValue(MDL_ZSCORE_SNR1,zscoreSNR1);
row.setValue(MDL_ZSCORE_SNR2,zscoreSNR2);
row.setValue(MDL_ZSCORE_HISTOGRAM,zscoreHist);
if (addToInput)
{
SF.setValue(MDL_ZSCORE,zscore,isort_1);
SF.setValue(MDL_ZSCORE_SHAPE1,zscoreShape1,isort_1);
SF.setValue(MDL_ZSCORE_SHAPE2,zscoreShape2,isort_1);
SF.setValue(MDL_ZSCORE_SNR1,zscoreSNR1,isort_1);
SF.setValue(MDL_ZSCORE_SNR2,zscoreSNR2,isort_1);
SF.setValue(MDL_ZSCORE_HISTOGRAM,zscoreHist,isort_1);
}
SFout.addRow(row);
}
//Sorting taking into account a given percentage
if (per > 0)
{
MultidimArray<int> sortedShape1,sortedShape2,sortedSNR1,sortedSNR2,sortedHist,
sortedShapeSF1,sortedShapeSF2,sortedSNR1SF,sortedSNR2SF,sortedHistSF;
sortedZscoreShape1.indexSort(sortedShape1);
sortedZscoreShape2.indexSort(sortedShape2);
sortedZscoreSNR1.indexSort(sortedSNR1);
sortedZscoreSNR2.indexSort(sortedSNR2);
sortedZscoreHist.indexSort(sortedHist);
size_t numPartReject = (size_t)std::floor((per/100)*SF.size());
for (size_t numPar = SF.size()-1; numPar > (SF.size()-numPartReject); --numPar)
{
int isort_1 = DIRECT_A1D_ELEM(sortedShape1,numPar);
SFout.getRow(row, isort_1);
row.setValue(MDL_ENABLED,-1);
SFout.setRow(row,isort_1);
isort_1 = DIRECT_A1D_ELEM(sortedShape2,numPar);
SFout.getRow(row, isort_1);
row.setValue(MDL_ENABLED,-1);
SFout.setRow(row,isort_1);
isort_1 = DIRECT_A1D_ELEM(sortedSNR1,numPar);
SFout.getRow(row, isort_1);
row.setValue(MDL_ENABLED,-1);
SFout.setRow(row,isort_1);
isort_1 = DIRECT_A1D_ELEM(sortedSNR2,numPar);
SFout.getRow(row, isort_1);
row.setValue(MDL_ENABLED,-1);
SFout.setRow(row,isort_1);
isort_1 = DIRECT_A1D_ELEM(sortedHist,numPar);
SFout.getRow(row, isort_1);
row.setValue(MDL_ENABLED,-1);
SFout.setRow(row,isort_1);
if (addToInput)
{
ZscoreShape1.indexSort(sortedShapeSF1);
ZscoreShape2.indexSort(sortedShapeSF2);
ZscoreSNR1.indexSort(sortedSNR1SF);
ZscoreSNR2.indexSort(sortedSNR2SF);
ZscoreHist.indexSort(sortedHistSF);
isort_1 = DIRECT_A1D_ELEM(sortedShapeSF1,numPar);
SF.getRow(row, isort_1);
row.setValue(MDL_ENABLED,-1);
SF.setRow(row,isort_1);
isort_1 = DIRECT_A1D_ELEM(sortedShapeSF2,numPar);
SF.getRow(row, isort_1);
row.setValue(MDL_ENABLED,-1);
SF.setRow(row,isort_1);
isort_1 = DIRECT_A1D_ELEM(sortedSNR1SF,numPar);
SF.getRow(row, isort_1);
row.setValue(MDL_ENABLED,-1);
SF.setRow(row,isort_1);
isort_1 = DIRECT_A1D_ELEM(sortedSNR2SF,numPar);
SF.getRow(row, isort_1);
row.setValue(MDL_ENABLED,-1);
SF.setRow(row,isort_1);
isort_1 = DIRECT_A1D_ELEM(sortedHistSF,numPar);
SF.getRow(row, isort_1);
row.setValue(MDL_ENABLED,-1);
SF.setRow(row,isort_1);
}
}
}
if (verbose==2)
fh_zind.close();
if (!fn_out.empty())
{
MetaData SFsorted;
SFsorted.sort(SFout,MDL_ZSCORE);
SFout.write(fn_out,MD_OVERWRITE);
}
if (addToInput)
{
MetaData SFsorted;
SFsorted.sort(SF,MDL_ZSCORE);
SFsorted.write(fn,MD_APPEND);
}
}
