private void calculateOrigin()
{
// TODO I am ignoring the possibility of passing in the origin for now and using the dot product calc for non orthoganality.
// The origin is perhaps used for cryoEM only and requires orthoganility
// CRSSTART is w05_NXSTART, w06_NYSTART, w07_NZSTART
// Cell dims w08_MX, w09_MY, w10_MZ;
// Map of indices from crs to xyz is w17_MAPC, w18_MAPR, w19_MAPS
EdVector vCRS = new EdVector();
for (int i = 0; i < 3; ++i)
{
int startVal = 0;
if (w17_MAPC == i)
{
startVal = w05_NXSTART;
}
else if (w18_MAPR == i)
{
startVal = w06_NYSTART;
}
else
{
startVal = w07_NZSTART;
}
vCRS.vector[i] = startVal;
}
vCRS.vector[0] /= w08_MX;
vCRS.vector[1] /= w09_MY;
vCRS.vector[2] /= w10_MZ;
_origin = _orthoMat.multiply(vCRS);
}
public DensityPoint getCRSFromXYZ(double x, double y, double z)
{
EdVector vXYZIn = new EdVector();
EdVector vCRS = new EdVector();
vXYZIn.vector[0] = x;
vXYZIn.vector[1] = y;
vXYZIn.vector[2] = z;
//If the axes are all orthogonal
if (w14_CELLB_X == 90 && w15_CELLB_Y == 90 && w16_CELLB_Z == 90)
{
for (int i = 0; i < 3; ++i)
{
double startVal = vXYZIn.vector[i] - _origin.vector[i];
startVal /= _cellDims[i] / _axisSampling[i];
vCRS.vector[i] = startVal;
}
}
else // they are not orthogonal
{
EdVector vFraction = _deOrthoMat.multiply(vXYZIn);
for (int i = 0; i < 3; ++i)
{
double val = vFraction.vector[i] * _axisSampling[i] - _crsStart[_map2xyz[i]];
vCRS.vector[i] = val;
}
}
double c = Convert.ToSingle(Math.Round(vCRS.vector[_map2crs[0]], 4));
double r = Convert.ToSingle(Math.Round(vCRS.vector[_map2crs[1]], 4));
double s = Convert.ToSingle(Math.Round(vCRS.vector[_map2crs[2]], 4));
DensityPoint dp = new DensityPoint(c, r, s, 0, "CRS");
return(dp);
}