double Miller::expectedRadius(double spotSize, double mosaicity, vec *hkl)
{
vec usedHKL;
if (hkl == NULL)
{
MatrixPtr newMatrix = MatrixPtr();
rotateMatrixHKL(latestHRot, latestKRot, 0, matrix, &newMatrix);
usedHKL = new_vector(h, k, l);
hkl = &usedHKL;
newMatrix->multiplyVector(hkl);
}
spotSize = fabs(spotSize);
double radMos = fabs(mosaicity) * M_PI / 180;
double distanceFromOrigin = length_of_vector(*hkl);
double spotSizeIncrease = fabs(radMos * distanceFromOrigin);
double radius = (spotSize + spotSizeIncrease);
return radius;
}
/**
Generates twinned/untwinned reflection IDs for easy searching.
*/
void Reflection::generateReflectionIds()
{
if (millerCount() == 0)
{
std::cout << "Warning! Miller count is 0" << std::endl;
}
int h = miller(0)->getH();
int k = miller(0)->getK();
int l = miller(0)->getL();
vec hkl = new_vector(h, k, l);
for (int i = 0; i < ambiguityCount(); i++)
{
MatrixPtr ambiguityMat = matrixForAmbiguity(i);
int asuH, asuK, asuL;
ccp4spg_put_in_asu(spaceGroup, hkl.h, hkl.k, hkl.l, &asuH, &asuK, &asuL);
vec hklAsu = new_vector(asuH, asuK, asuL);
ambiguityMat->multiplyVector(&hklAsu);
int newId = reflectionIdForMiller(hklAsu);
reflectionIds.push_back(newId);
}
}
vec Miller::getTransformedHKL(MatrixPtr matrix)
{
vec hkl = new_vector(h, k, l);
matrix->multiplyVector(&hkl);
return hkl;
}
void Miller::recalculatePartiality(MatrixPtr rotatedMatrix, double mosaicity,
double spotSize, double wavelength, double bandwidth, double exponent, bool binary)
{
if (model == PartialityModelFixed)
{
return;
}
if (model == PartialityModelBinary)
{
// binary = true;
}
vec hkl = new_vector(h, k, l);
rotatedMatrix->multiplyVector(&hkl);
this->wavelength = getEwaldSphereNoMatrix(hkl);
double tempPartiality = partialityForHKL(hkl, mosaicity,
spotSize, wavelength, bandwidth, exponent, binary);
if (binary && tempPartiality == 1.0)
return;
double normPartiality = 1;
if (normalised && tempPartiality > 0)
{
normPartiality = calculateNormPartiality(rotatedMatrix, mosaicity, spotSize, wavelength, bandwidth, exponent);
}
else
{
partiality = 0;
return;
}
partiality = tempPartiality / normPartiality;
if (partiality > 1.2)
partiality = 0;
if (partiality > 1.0)
partiality = 1;
if (partiality > 1 && std::isfinite(partiality))
{
std::cout << "Partiality: " << partiality << std::endl;
}
if ((!std::isfinite(partiality)) || (partiality != partiality))
{
partiality = 0;
}
}
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();
}
double Miller::calculateNormPartiality(MatrixPtr rotatedMatrix, double mosaicity,
double spotSize, double wavelength, double bandwidth, double exponent)
{
vec hkl = new_vector(h, k, l);
rotatedMatrix->multiplyVector(&hkl);
double d = length_of_vector(hkl);
double newH = 0;
double newK = sqrt((4 * pow(d, 2) - pow(d, 4) * pow(wavelength, 2)) / 4);
double newL = 0 - pow(d, 2) * wavelength / 2;
vec newHKL = new_vector(newH, newK, newL);
double normPartiality = partialityForHKL(newHKL, mosaicity,
spotSize, wavelength, bandwidth, exponent);
return normPartiality;
}
bool Miller::crossesBeamRoughly(MatrixPtr rotatedMatrix, double mosaicity,
double spotSize, double wavelength, double bandwidth)
{
vec hkl = new_vector(h, k, l);
rotatedMatrix->multiplyVector(&hkl);
double inwards_bandwidth = 0; double outwards_bandwidth = 0;
limitingEwaldWavelengths(hkl, mosaicity, spotSize, wavelength, &outwards_bandwidth, &inwards_bandwidth);
double limit = 2 * bandwidth;
double inwardsLimit = wavelength + limit;
double outwardsLimit = wavelength - limit;
if (outwards_bandwidth > inwardsLimit || inwards_bandwidth < outwardsLimit)
{
partiality = 0;
return false;
}
partiality = 1;
return true;
}
void Miller::positionOnDetector(MatrixPtr transformedMatrix, int *x,
int *y)
{
double x_coord = 0;
double y_coord = 0;
vec hkl = new_vector(h, k, l);
transformedMatrix->multiplyVector(&hkl);
std::pair<double, double> coord = getImage()->reciprocalCoordinatesToPixels(hkl);
x_coord = coord.first;
y_coord = coord.second;
bool even = shoebox->isEven();
int intLastX = int(x_coord);
int intLastY = int(y_coord);
if (even)
{
intLastX = round(x_coord);
intLastY = round(y_coord);
}
lastX = x_coord;
lastY = y_coord;
if (!Panel::shouldUsePanelInfo())
{
int search = indexer->getSearchSize();
getImage()->focusOnAverageMax(&intLastX, &intLastY, search, peakSize, even);
shift = std::make_pair(intLastX + 0.5 - x_coord, intLastY + 0.5 - y_coord);
*x = intLastX;
*y = intLastY;
}
else
{
int search = indexer->getSearchSize();
Coord bestShift = Panel::shiftForMiller(this);
if (bestShift.first != FLT_MAX)
{
double shiftedX = lastX + bestShift.first;
double shiftedY = lastY + bestShift.second;
int xInt = shiftedX;
int yInt = shiftedY;
getImage()->focusOnAverageMax(&xInt, &yInt, search, peakSize, even);
shift = std::make_pair(xInt + 0.5 - x_coord, yInt + 0.5 - y_coord);
*x = xInt;
*y = yInt;
}
else
{
int search = indexer->getSearchSize();
getImage()->focusOnAverageMax(&intLastX, &intLastY, search, peakSize, even);
*x = intLastX;
*y = intLastY;
}
}
}
