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);
}
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 void movePoint(double distance, EdVector direction)
{
//TODO for now just add the amount to every point
XYZ.x += distance * direction.x;
XYZ.y += distance * direction.y;
XYZ.z += distance * direction.z;
}
public EdVector add(EdVector B)
{
double px = x + B.x;
double py = y + B.y;
double pz = z + B.z;
return(new EdVector(px, py, pz));
}
public EdVector subtract(EdVector B)
{
double px = x - B.x;
double py = y - B.y;
double pz = z - B.z;
return(new EdVector(px, py, pz));
}
public EdVector crossProduct(EdVector B)
{
double px = (y * B.z) - (z * B.y);
double py = (z * B.x) - (x * B.z);
double pz = (x * B.y) - (y * B.x);
return(new EdVector(px, py, pz));
}
public EdVector findOrthogonalToLine(EdVector line, EdVector plane)
{
EdVector O1 = findOrthogonalToPlane(this, line, plane);
EdVector V1 = new EdVector(this.x + O1.x, this.y + O1.y, this.z + O1.z);
EdVector O2 = findOrthogonalToPlane(this, line, V1);
return(O2);
}
public double distance(EdVector B)
{
double px = Math.Pow(x - B.x, 2);
double py = Math.Pow(y - B.y, 2);
double pz = Math.Pow(z - B.z, 2);
return(Math.Sqrt(px + py + pz));
}
public double dotProduct(EdVector B)
{
double px = x * B.x;
double py = y * B.y;
double pz = z * B.z;
return(px + py + pz);
}
public EdVector multiply(EdVector v)
{//http://mlwiki.org/index.php/Matrix-Vector_Multiplication
EdVector Ax = getColumn(0).scale(v.x);
EdVector Ay = getColumn(1).scale(v.y);
EdVector Az = getColumn(2).scale(v.z);
EdVector A = Ax.add(Ay).add(Az);
return(A);
}
public EdVector getColumn(int col)
{
EdVector colv = new EdVector();
colv.vector[0] = matrix[0, col];
colv.vector[1] = matrix[1, col];
colv.vector[2] = matrix[2, col];
return(colv);
}
public EdVector findOrthogonalToPlane(EdVector A, EdVector B, EdVector C)
{
EdVector AB = new EdVector(B.x - A.x, B.y - A.y, B.z - A.z);
EdVector AC = new EdVector(C.x - A.x, C.y - A.y, C.z - A.z);
EdVector O = AB.crossProduct(AC);
O.normalise();
return(O);
}
public DensityPoint getXYZFromCRS(double c, double r, double s)
{
EdVector vXYZ = new EdVector();
EdVector vCRSIn = new EdVector();
vCRSIn.vector[0] = c;
vCRSIn.vector[1] = r;
vCRSIn.vector[2] = s;
//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 = vCRSIn.vector[_map2xyz[i]];
startVal *= _cellDims[i] / _axisSampling[i];
startVal += _origin.vector[i];
vXYZ.vector[i] = startVal;
}
}
else // they are not orthogonal
{
EdVector vCRS = new EdVector();
for (int i = 0; i < 3; ++i)
{
Double startVal = 0;
if (w17_MAPC == i)
{
startVal = w05_NXSTART + c;
}
else if (w18_MAPR == i)
{
startVal = w06_NYSTART + r;
}
else
{
startVal = w07_NZSTART + s;
}
vCRS.vector[i] = startVal;
}
vCRS.vector[0] /= w08_MX;
vCRS.vector[1] /= w09_MY;
vCRS.vector[2] /= w10_MZ;
vXYZ = _orthoMat.multiply(vCRS);
}
DensityPoint dp = new DensityPoint(Convert.ToSingle(vXYZ.vector[0]), Convert.ToSingle(vXYZ.vector[1]), Convert.ToSingle(vXYZ.vector[2]), 0, "XYZ");
return(dp);
}
