double Reflection::meanIntensityWithExclusion(std::string *filename, int start, int end)
{
if (filename == NULL)
return meanIntensity(start, end);
if (end == 0)
end = acceptedCount();
double total_intensity = 0;
double weight = 0;
int accepted = acceptedCount();
for (int i = start; i < end; i++)
{
MillerPtr miller = this->acceptedMiller(i);
if (accepted > 2 && miller->getFilename() == *filename)
continue;
total_intensity += miller->intensity();
weight += 1;
}
total_intensity /= weight;
return total_intensity;
}
double Reflection::meanSigma(bool friedel)
{
int num = (int)millerCount();
int count = 0;
double total_sigi = 0;
for (int i = 0; i < num; i++)
{
MillerPtr aMiller = miller(i);
if (aMiller->accepted())
{
total_sigi += aMiller->getSigma();
count++;
}
}
total_sigi /= count;
if (total_sigi == 0)
return nan(" ");
return total_sigi;
}
double Reflection::meanIntensity(bool withCutoff, int start, int end)
{
if (end == 0)
end = withCutoff ? acceptedCount() : millerCount();
double total_intensity = 0;
double total_weights = 0;
for (int i = start; i < end; i++)
{
MillerPtr miller = withCutoff ? this->acceptedMiller(i) : this->miller(i);
double weight = miller->getWeight(withCutoff);
double intensity = miller->intensity(withCutoff);
if (weight <= 0)
continue;
total_intensity += intensity * weight;
total_weights += weight;
}
total_intensity /= total_weights;
return total_intensity;
}
void Shoebox::complexShoebox(double wavelength, double bandwidth, double radius)
{
MillerPtr tempMiller = getMiller();
if (!tempMiller)
{
return;
}
MatrixPtr mat;
mat = tempMiller->getMatrix();
vec hkl = new_vector(tempMiller->getH(), tempMiller->getK(), tempMiller->getL());
mat->multiplyVector(&hkl);
double hk = sqrt(hkl.h * hkl.h + hkl.k * hkl.k);
double maxHK = hk + radius;
double minHK = hk - radius;
double minWave = wavelength - bandwidth * bandwidthMultiplier;
double maxWave = wavelength + bandwidth * bandwidthMultiplier;
double max_mm = (maxHK * detectorDistance / (1 / maxWave + hkl.l));
double min_mm = (minHK * detectorDistance / (1 / minWave + hkl.l));
double width_mm = (radius * detectorDistance / (1 / wavelength));
double mmDiff = max_mm - min_mm;
double widthLeak = 1 * pixelLeak;
double pixelHeight = mmDiff / mmPerPixel + pixelLeak;
double pixelWidth = 2 * width_mm / mmPerPixel + widthLeak;
double angle = cartesian_to_angle(hkl.h, hkl.k);
angle += M_PI / 2;
Box smallBox;
Box newShoebox;
compressBigShoebox(pixelWidth, pixelHeight, angle, smallBox);
chopBox(smallBox);
centreShoebox(smallBox);
putBoxOnPaddedBackground(smallBox, newShoebox);
shoebox = newShoebox;
printShoebox();
}
void Reflection::addMiller(MillerPtr miller)
{
miller->setResolution(resolution);
millers.push_back(miller);
if (reflectionIds.size() == 0)
{
generateReflectionIds();
}
}
double Reflection::meanIntensity(int start, int end)
{
if (end == 0)
end = acceptedCount();
double total_intensity = 0;
double weight = 0;
for (int i = start; i < end; i++)
{
MillerPtr miller = this->acceptedMiller(i);
total_intensity += miller->intensity();
weight += 1;
}
total_intensity /= weight;
return total_intensity;
}
double Reflection::meanPartiality(bool withCutoff)
{
int num = millerCount();
double total_partiality = 0;
int count = 0;
for (int i = 0; i < num; i++)
{
MillerPtr miller = millers[i];
if ((miller->accepted() && withCutoff) || !withCutoff)
{
total_partiality += miller->getPartiality();
count++;
}
}
total_partiality /= count;
return total_partiality;
}
double Miller::averageRawIntensity(vector<MillerPtr> millers)
{
double allIntensities = 0;
int num = 0;
for (int i = 0; i < millers.size(); i++)
{
MillerPtr miller = millers[i];
double anIntensity = miller->getRawIntensity();
if (anIntensity != anIntensity)
continue;
allIntensities += anIntensity;
num++;
}
allIntensities /= num;
return allIntensities;
}
double Reflection::meanSigma()
{
int num = (int)millers.size();
int count = 0;
double total_sigi = 0;
for (int i = 0; i < num; i++)
{
MillerPtr miller = millers[i];
if (miller->accepted())
{
total_sigi += miller->getSigma();
count++;
}
}
total_sigi /= count;
return total_sigi;
}
double Reflection::meanWeight()
{
int num = (int)millers.size();
int count = 0;
double total_weight = 0;
for (int i = 0; i < num; i++)
{
MillerPtr miller = millers[i];
if (miller->accepted())
{
total_weight += 1 / pow(miller->getSigma(), 2);
count++;
}
}
total_weight /= count;
return total_weight;
}
double Reflection::meanWeight(bool withCutoff)
{
int num = (int)millerCount();
int count = 0;
double total_weight = 0;
for (int i = 0; i < num; i++)
{
MillerPtr miller = millers[i];
if ((miller->accepted() && withCutoff) || !withCutoff)
{
total_weight += miller->getWeight(withCutoff);
count++;
}
}
total_weight /= count;
return total_weight;
}
Shoebox::Shoebox(MillerPtr parent)
{
miller = parent;
if (parent)
{
ImagePtr image = parent->getImage();
mmPerPixel = image->getMmPerPixel();
detectorDistance = image->getDetectorDistance();
}
pixelLeak = FileParser::getKey("PIXEL_LEAK", PIXEL_LEAK);
bandwidthMultiplier = FileParser::getKey("SHOEBOX_BANDWIDTH_MULTIPLIER", SHOEBOX_BANDWIDTH_MULTIPLIER);
}
/**
Takes the h,k,l values, flips the Miller and folds back onto the asymmetric unit. If the Miller indices are the same, it is twinned. (Not suitable for non-hemihedral twinning at the moment)
*/
bool Reflection::isTwinned()
{
if (millerCount() > 0)
{
int h, k, l = 0;
int trueH = miller(0)->getH();
int trueK = miller(0)->getK();
int trueL = miller(0)->getL();
miller(0)->flip();
MillerPtr firstMiller = miller(0);
ccp4spg_put_in_asu(spaceGroup, firstMiller->getH(),
firstMiller->getK(), firstMiller->getL(), &h, &k, &l);
miller(0)->flip();
return (h == trueH && k == trueK && l == trueL);
}
else
{
return false;
}
}
void Reflection::reflectionDescription()
{
int acceptedCount = 0;
std::ostringstream logged;
for (int i = 0; i < millerCount(); i++)
{
MillerPtr miller = this->miller(i);
logged << miller->getH() << "\t" << miller->getK() << "\t" << miller->getL() << "\t"
<< miller->getRawIntensity() << "\t" << miller->getPartiality()
<< "\t" << miller->getSigma() << "\t" << miller->getFilename()
<< std::endl;
if (miller->accepted())
acceptedCount++;
}
logged << std::endl;
Logger::mainLogger->addStream(&logged);
}
void GraphDrawer::plotPolarisation(vector<MtzPtr> mtzs)
{
int count = 36;
int divide = 360 / count;
std::map<int, double> histogram;
std::map<int, int> counts;
for (int i = 0; i < mtzs.size(); i++)
{
for (int j = 0; j < mtzs[i]->reflectionCount(); j++)
{
if (!mtzs[i]->reflection(j)->betweenResolutions(1.8, 1.4))
continue;
for (int k = 0; k < mtzs[i]->reflection(j)->millerCount(); k++)
{
MillerPtr miller = mtzs[i]->reflection(j)->miller(k);
if (miller->getRawIntensity() < 0)
continue;
vec hkl = new_vector(miller->getH(), miller->getK(), miller->getL());
mtzs[i]->getMatrix()->multiplyVector(&hkl);
double angle = cartesian_to_angle(hkl.h, hkl.k);
double degrees = angle * 180 / M_PI;
int category = (int)(degrees / divide) * divide;
if (histogram.count(category) == 0)
{
histogram[category] = 0;
counts[category] = 0;
}
histogram[category] += miller->getRawIntensity();
counts[category]++;
}
}
}
vector<double> xs, ys;
GraphMap graphMap;
graphMap["yMin"] = 0;
graphMap["yMax"] = 200;
graphMap["title"] = "Average raw intensity vs angle on detector";
graphMap["xTitle"] = "Angle on detector";
graphMap["yTitle"] = "Average raw intensity";
int num = 0;
for (int i = 0; i <= 0; i++)
{
for (std::map<int, double>::iterator it = histogram.begin(); it != histogram.end(); it++)
{
if (i == 0)
histogram[it->first] /= counts[it->first];
xs.push_back(it->first + (i * 360));
ys.push_back(histogram[it->first]);
num++;
}
}
std::cout << "Number of X values: " << num << std::endl;
plot("polarisation", graphMap, xs, ys);
}
