//(c) Chernysheva, TEST(Matrix, ToStringNotNullBits)
//------->>>>>>>>>-----------------
//перевод матрицы в строку,
//возвращает строку c номерами строк и столбцов с ненулевыми значениям
//в формате {строка, столбец}
string Matrix::ToStringNotNullBits()
{
string res = "";
switch (CodeWord)
{
case ON_LINE:
for (int i = 0; i < RowCount; i++)
{
for (int j = 0; j < ColCount; j++)
{
bool val = this->getBit(i, j);
if (val)
res += "{" + i_to_str(i) + "," + i_to_str(j) + "}";
}
}
break;
case ON_COLUMN:
Matrix buf(*this);
buf.conversionMatrix();
for (int i = 0; i < buf.getRowCount(); i++)
{
for (int j = 0; j < buf.getColCount(); j++)
{
bool val = buf.getBit(i, j);
if (val)
res += "{" + i_to_str(i) + "," + i_to_str(j) + "}";
}
}
break;
}
return res;
}
void Deconvoluter::process()
{
std::string file = FileParser::getKey("TWINNED_MTZ", std::string(""));
wangEnvName = FileParser::getKey("WANG_ENVELOPE_OUTPUT", std::string("wang.env"));
molUnitName = FileParser::getKey("MOL_UNIT_ENVELOPE_OUTPUT", std::string("mol_unit.env"));
tempFftMapName = FileParser::getKey("TEMP_FFT_MAP", std::string("temp_fft.map"));
tempAveMapName = FileParser::getKey("TEMP_AVERAGE_MAP", std::string("temp_ave.map"));
tempMtzName = FileParser::getKey("TEMP_AVERAGE_MTZ", std::string("temp_ave.mtz"));
tempSortedMtzName = FileParser::getKey("TEMP_AVERAGE_SORTED_MTZ", std::string("temp_sorted_ave.mtz"));
cadMtzName = FileParser::getKey("TEMP_CAD_MTZ", std::string("temp_cad.mtz"));
fsmeltMtzName = FileParser::getKey("TEMP_FSMELT_MTZ", std::string("temp_fsmelt.mtz"));
std::string fObsLab = FileParser::getKey("LABIN_AMPLITUDES", std::string("F"));
std::string fCalcLab = FileParser::getKey("LABOUT_CALC_AMPLITUDES", std::string("FC"));
std::string ncsDefs = FileParser::getKey("NCS_DEFINITIONS_FILE", std::string(""));
std::vector<double> ccAll, ccSinglets, rAll, rSinglets;
if (ncsDefs.length() == 0)
{
std::cout << "Warning! NCS definitions file missing. Please specify file in GAP format using keyword NCS_DEFINITIONS_FILE" << std::endl;
exit(1);
}
int bins = 20;
int maxCycles = FileParser::getKey("MAXIMUM_CYCLES", 10);
if (file == "")
{
std::cout << "Twinned MTZ has not been provided, please provide file path under keyword TWINNED_MTZ" << std::endl;
exit(1);
}
// loading original, twinned MTZ into memory.
originalMtz = MtzPtr(new MtzManager(file));
originalMtz->loadReflections(false);
MtzManager::setReference(&*originalMtz);
spaceGroup = FileParser::getKey("SPACE_GROUP", originalMtz->getLowGroup()->spg_num);
std::cout << "Loaded original MTZ file " << file << std::endl;
bool skipFirst = FileParser::getKey("SKIP_FIRST_CYCLE", false);
int beginning = FileParser::getKey("RESUME_FROM_CYCLE", 0);
if (beginning > 0) skipFirst = true;
for (int i = beginning; i < maxCycles; i++)
{
if (i > beginning || (i == beginning && !skipFirst))
{
fastFourierTransform(file, tempFftMapName, (i > 0));
gapEnvelope(tempFftMapName);
gapAverage(tempFftMapName, wangEnvName, molUnitName);
map_to_sf(tempAveMapName, tempMtzName);
sort_mtz(tempMtzName, tempSortedMtzName);
cad(tempSortedMtzName, cadMtzName);
fsmelt(file, cadMtzName, fsmeltMtzName);
}
MtzPtr nextMtz = MtzPtr(new MtzManager(fsmeltMtzName));
nextMtz->loadReflections(true); // fc in "intensity" and f in "fc"...
nextMtz->applyScaleFactorsForBins(bins);
nextMtz->individualDetwinningScales((i == maxCycles - 1));
nextMtz->copyOtherAmplitudesFromReference();
file = "detwinned_cycle_" + i_to_str(i) + ".mtz";
nextMtz->writeToFile(file);
std::cout << "******************************" << std::endl;
std::cout << "** CORRELATION (ALL) **" << std::endl;
std::cout << "******************************" << std::endl;
std::cout << std::endl << "Correlation between all scaled data and original twinned data" << std::endl;
std::cout << std::endl << std::setw(15) << "Low res " << std::setw(15) << "High res " << std::setw(15) << "Correl" << std::setw(15) << "Num refl" << std::endl;
ccAll.push_back(nextMtz->correlationWithManager(&*originalMtz, false, false, 0, 0, bins, NULL, false));
std::cout << "*******************************" << std::endl;
std::cout << "** CORRELATION (SINGLETS) **" << std::endl;
std::cout << "*******************************" << std::endl;
std::cout << std::endl << "Correlation between singlet scaled data and original twinned data" << std::endl;
std::cout << std::endl << std::setw(15) << "Low res " << std::setw(15) << "High res " << std::setw(15) << "Correl" << std::setw(15) << "Num refl" << std::endl;
ccSinglets.push_back(nextMtz->correlationWithManager(&*originalMtz, false, false, 0, 0, bins, NULL, true));
std::cout << "******************************" << std::endl;
std::cout << "** R FACTOR (ALL) **" << std::endl;
std::cout << "******************************" << std::endl;
std::cout << std::endl << "R factor between all scaled data and original twinned data" << std::endl;
std::cout << std::endl << std::setw(15) << "Low res " << std::setw(15) << "High res " << std::setw(15) << "Correl" << std::setw(15) << "Num refl" << std::endl;
rAll.push_back(nextMtz->rSplitWithManager(&*originalMtz, false, false, 0, 0, bins, NULL, false));
std::cout << "*******************************" << std::endl;
std::cout << "** R FACTOR (SINGLETS) **" << std::endl;
std::cout << "*******************************" << std::endl;
std::cout << std::endl << "R factor between singlet scaled data and original twinned data" << std::endl;
std::cout << std::endl << std::setw(15) << "Low res " << std::setw(15) << "High res " << std::setw(15) << "Correl" << std::setw(15) << "Num refl" << std::endl;
rSinglets.push_back(nextMtz->rSplitWithManager(&*originalMtz, false, false, 0, 0, bins, NULL, true));
}
std::cout << "*******************************" << std::endl;
std::cout << "** END OF DECONVOLUTION **" << std::endl;
std::cout << "*******************************" << std::endl;
std::cout << std::endl << "Summary of deconvolution:" << std::endl << std::endl;
std::cout << "Cycle\tCCall\tCCsinglets\tRall\tRsinglets" << std::endl;
for (int i = 0; i < ccAll.size(); i++)
{
std::cout << i << "\t" << ccAll[i] << "\t" << ccSinglets[i] << "\t" << rAll[i] << "\t" << rSinglets[i] << std::endl;
}
}
void GraphDrawer::partialityPlot(std::string filename, GraphMap properties, double maxRes)
{
double correl = mtz->correlation();
mtz->setActiveAmbiguity(1);
double invCorrel = mtz->correlation();
std::cout << "Ambiguity 0: " << correl << ", ambiguity 1: " << invCorrel << std::endl;
if (correl > invCorrel)
mtz->setActiveAmbiguity(0);
double gradient = mtz->gradientAgainstManager(MtzManager::getReferenceManager());
mtz->applyScaleFactor(gradient);
properties["title"] = "Partiality plot " + mtz->getFilename();
properties["xTitle"] = "Wavelength (Å)";
properties["yTitle"] = "Fraction of merged data set (%)";
properties["plotType"] = "fill";
vector<double> resolutions;
StatisticsManager::generateResolutionBins(0, maxRes, 4, &resolutions);
vector<std::string> files;
vector<Partial> partials;
StatisticsManager::twoImagePartialityStatsWritten(&partials,
&MtzManager::getReferenceManager(), &mtz);
std::cout << "Total number of reflections in MTZ: " << partials.size() << std::endl;
double maxPercentage = 1000;
std::sort(partials.begin(), partials.end(), sortByPercentage);
maxPercentage = partials[partials.size() - 10].percentage;
if (maxPercentage < 500 || !std::isfinite(maxPercentage))
maxPercentage = 500;
maxPercentage = 500;
std::sort(partials.begin(), partials.end(), sortByWavelength);
double minX = partials[50].wavelength;
double maxX = partials[partials.size() - 50].wavelength;
double middle = partials[partials.size() / 2].wavelength;
double wantedWidth = 0.08;
// std::cout << "minX: " << minX << ", maxX: " << maxX << ", middle: " << middle << std::endl;
if (maxX - minX > wantedWidth)
{
maxX = middle + wantedWidth / 2;
minX = middle - wantedWidth / 2;
}
int resCount = (int)resolutions.size();
properties["xMin"] = minX;
properties["xMax"] = maxX;
properties["yMin2"] = 0;
properties["yMax2"] = 5.0;
properties["yMax"] = maxPercentage;
vector<double> xs, xs2, xs3, xs4, ys, ys2, ys3, ys4, scatterX, scatterY;
std::cout << std::setw(12) << "Low res" << std::setw(12) << "High res" << std::setw(12) << "Num refl." << std::endl;
for (int shell = 0; shell < resCount - 1; shell++)
{
xs.clear();
ys.clear();
xs2.clear();
ys2.clear();
xs3.clear();
ys3.clear();
double lowRes = 1 / resolutions[shell];
double highRes = 1 / resolutions[shell + 1];
std::ofstream partLog;
partLog.open("partiality_" + i_to_str(shell) + ".csv");
partLog << "h,k,l,wavelength,partiality,percentage,intensity,resolution" << std::endl;
int count = 0;
for (int i = 0; i < partials.size(); i++)
{
if (partials[i].resolution > lowRes
&& partials[i].resolution < highRes)
{
if (partials[i].wavelength != partials[i].wavelength
|| partials[i].percentage != partials[i].percentage
|| partials[i].partiality != partials[i].partiality)
continue;
if (partials[i].percentage > maxPercentage)
continue;
double h = partials[i].miller->getH();
double k = partials[i].miller->getK();
double l = partials[i].miller->getL();
double wavelength = partials[i].wavelength;
double partiality = partials[i].partiality;
double percentage = partials[i].percentage;
double intensity = partials[i].miller->getRawestIntensity();
double resolution = partials[i].resolution;
partLog << h << "," << k << "," << l << "," << wavelength << "," << partiality << "," <<
percentage << "," << intensity << "," << resolution << std::endl;
count++;
}
}
partLog.close();
std::cout << std::setw(12) << 1 / lowRes << std::setw(12) << 1 / highRes << std::setw(12) << count
<< std::endl;
}
/*
int milliseconds = 1200 / resCount;
std::string animate = "convert -delay " + i_to_str(milliseconds) + " -loop 0 ";
std::string rmv = "rm ";
for (int i = 0; i < resCount - 1; i++)
{
animate += files[i] + " ";
rmv += files[i] + " ";
}
rmv += "\n";
std::string fullName = generateFilename(filename, "gif");
animate += fullName;
animate += "\n";
// std::cout << animate << std::endl;
std::string all = animate + rmv;
system(all.c_str());
std::cout << "N: plot " << fullName << std::endl;
properties["title"] = "Partiality scatter";
properties["xTitle"] = "Predicted partiality";
properties["yTitle"] = "Fraction of merged data set (%)";
properties["plotType"] = "point";
properties["xMin"] = 0;
properties["xMax"] = 1.2;
properties["yMin"] = 0;
properties["yMax"] = maxPercentage;
*/
// plot(filename + "_scatter", properties, scatterX, scatterY);
}