/**
* Returns selected information for a "peak" at QLabFrame.
*
* @param qFrame An arbitrary position in Q-space. This does not have to
*be the
* position of a peak.
* @param labCoords Set true if the position is in the lab coordinate system,
*false if
* it is in the sample coordinate system.
* @return a vector whose elements contain different information about the
*"peak" at that position.
* each element is a pair of description of information and the string
*form for the corresponding
* value.
*/
int PeaksWorkspace::peakInfoNumber(Kernel::V3D qFrame, bool labCoords) const {
std::vector<std::pair<std::string, std::string>> Result;
std::ostringstream oss;
oss << std::setw(12) << std::fixed << std::setprecision(3) << (qFrame.norm());
std::pair<std::string, std::string> QMag("|Q|", oss.str());
Result.push_back(QMag);
oss.str("");
oss.clear();
oss << std::setw(12) << std::fixed << std::setprecision(3)
<< (2.0 * M_PI / qFrame.norm());
std::pair<std::string, std::string> dspc("d-spacing", oss.str());
oss.str("");
oss.clear();
Result.push_back(dspc);
int seqNum = -1;
double minDist = 10000000;
for (int i = 0; i < getNumberPeaks(); i++) {
Peak pk = getPeak(i);
V3D Q = pk.getQLabFrame();
if (!labCoords)
Q = pk.getQSampleFrame();
double D = qFrame.distance(Q);
if (D < minDist) {
minDist = D;
seqNum = i + 1;
}
}
return seqNum;
}
/**
* Determines whether point is within the object or on the surface
* @param point :: Point to be tested
* @returns true if point is within object or on surface
*/
bool MeshObject::isValid(const Kernel::V3D &point) const {
BoundingBox bb = getBoundingBox();
if (!bb.isPointInside(point)) {
return false;
}
Kernel::V3D direction(0.0, 0.0, 1.0); // direction to look for intersections
std::vector<Kernel::V3D> intersectionPoints;
std::vector<TrackDirection> entryExitFlags;
getIntersections(point, direction, intersectionPoints, entryExitFlags);
if (intersectionPoints.empty()) {
return false;
}
// True if point is on surface
for (const auto &intersectionPoint : intersectionPoints) {
if (point.distance(intersectionPoint) < M_TOLERANCE) {
return true;
}
}
// Look for nearest point then check its entry-exit flag
double nearestPointDistance = point.distance(intersectionPoints[0]);
size_t nearestPointIndex = 0;
for (size_t i = 1; i < intersectionPoints.size(); ++i) {
if (point.distance(intersectionPoints[i]) < nearestPointDistance) {
nearestPointDistance = point.distance(intersectionPoints[i]);
nearestPointIndex = i;
}
}
return (entryExitFlags[nearestPointIndex] == TrackDirection::LEAVING);
}
std::string makeAxisName(const Kernel::V3D &Dir,
const std::vector<std::string> &QNames) {
double eps(1.e-3);
Kernel::V3D absDir(fabs(Dir.X()), fabs(Dir.Y()), fabs(Dir.Z()));
std::string mainName;
if ((absDir[0] >= absDir[1]) && (absDir[0] >= absDir[2])) {
mainName = QNames[0];
} else if (absDir[1] >= absDir[2]) {
mainName = QNames[1];
} else {
mainName = QNames[2];
}
std::string name("["), separator = ",";
for (size_t i = 0; i < 3; i++) {
if (i == 2)
separator = "]";
if (absDir[i] < eps) {
name += "0" + separator;
continue;
}
if (Dir[i] < 0) {
name += "-";
}
if (std::fabs(absDir[i] - 1) < eps) {
name.append(mainName).append(separator);
continue;
}
name.append(sprintfd(absDir[i], eps)).append(mainName).append(separator);
}
return name;
}
/**
* Return the XML for a sphere.
*/
std::string sphereXML(double radius, const Kernel::V3D ¢re, const std::string &id) {
std::ostringstream xml;
xml << "<sphere id=\"" << id << "\">"
<< "<centre x=\"" << centre.X() << "\" y=\"" << centre.Y() << "\" z=\""
<< centre.Z() << "\" />"
<< "<radius val=\"" << radius << "\" />"
<< "</sphere>";
return xml.str();
}
/**
Calculate if the point R is on
the cone (Note: have to be careful here
since angle calcuation calcuates an angle.
We need a distance for tolerance!)
@param R :: Point to check
@return 1 if on surface and 0 if not not on surface
*/
int Cone::onSurface(const Kernel::V3D &R) const {
const Kernel::V3D cR = R - Centre;
double rptAngle = cR.scalar_prod(Normal);
rptAngle *= rptAngle / cR.scalar_prod(cR);
const double eqn(sqrt(rptAngle));
return (fabs(eqn - cangle) > Tolerance) ? 0 : 1;
}
/**
* Set the new detector position given the r,theta and phi.
* @param detectorInfo :: Reference to the DetectorInfo
* @param index :: Index into detectorInfo
* @param l2 :: A single l2
* @param theta :: A single theta
* @param phi :: A single phi
*/
void UpdateInstrumentFromFile::setDetectorPosition(
Geometry::DetectorInfo &detectorInfo, const size_t index, const float l2,
const float theta, const float phi) {
if (m_ignoreMonitors && detectorInfo.isMonitor(index))
return;
Kernel::V3D pos;
pos.spherical(l2, theta, phi);
detectorInfo.setPosition(index, pos);
}
/**
Calculate if the point R is within
the cone (return -1) or outside,
(return 1)
\todo NEEDS ON SURFACE CALCULATING::
waiting for a point to cone distance function
@param R :: Point to determine if in/out of cone
@return Side of R
*/
int Cone::side(const Kernel::V3D &R) const {
const Kernel::V3D cR = R - Centre;
double rptAngle = cR.scalar_prod(Normal);
rptAngle *= rptAngle / cR.scalar_prod(cR);
const double eqn(sqrt(rptAngle));
if (fabs(eqn - cangle) < Tolerance)
return 0;
return (eqn > cangle) ? 1 : -1;
}
/// Returns 2 theta (scattering angle w.r.t. to beam direction).
double DetectorInfo::twoTheta(const size_t index) const {
const Kernel::V3D samplePos = samplePosition();
const Kernel::V3D beamLine = samplePos - sourcePosition();
if (beamLine.nullVector()) {
throw Kernel::Exception::InstrumentDefinitionError(
"Source and sample are at same position!");
}
return getDetector(index).getTwoTheta(samplePos, beamLine);
}
double Line::distance(const Kernel::V3D &A) const
/**
Distance of a point from the line
@param A :: test Point
@return absolute distance (not signed)
*/
{
const double lambda = Direct.scalar_prod(A - Origin);
Kernel::V3D L = getPoint(lambda);
L -= A;
return L.norm();
}
int Line::lambdaPair(
const int ix,
const std::pair<std::complex<double>, std::complex<double>> &SQ,
std::list<Kernel::V3D> &PntOut) const
/**
Helper function to decide which roots to take.
The assumption is that lambda has been solved by quadratic
equation and we require the points that correspond to these
values.
Note: have changed this so that only positive roots are returned.
This makes the quadratic solutions consistent with the ones returned
when asking if a line hits a plane. It is not clear if some other use
cases exist.
@param ix : number of solutions in SQ (0,1,2)
@param SQ : solutions to lambda (the distance along the line
@param PntOut : Output vector of points (added to)
@return Number of real unique points found.
*/
{
// check results
if (ix < 1)
return 0;
int nCnt(0); // number of good points
Kernel::V3D Ans;
if (SQ.first.imag() == 0.0 && SQ.first.real() >= 0.0) // +ve roots only
{
const double lambda = SQ.first.real();
Kernel::V3D Ans = getPoint(lambda);
PntOut.push_back(Ans);
if (ix < 2) // only one unique root.
return 1;
nCnt = 1;
}
if (SQ.second.imag() == 0.0 && SQ.second.real() >= 0.0) // +ve roots only
{
const double lambda = SQ.second.real();
if (!nCnt) // first point wasn't good.
{
PntOut.push_back(getPoint(lambda));
return 1;
}
Kernel::V3D Ans2 = getPoint(lambda);
// If points too close return only 1 item.
if (Ans.distance(Ans2) < Tolerance)
return 1;
PntOut.push_back(Ans2);
return 2;
}
return 0; // both point imaginary
}
/**
* Estalish if points are coplanar.
* @param vertices : All vertices to consider
* @return : Return True only if all coplanar
*/
bool MeshObject2D::pointsCoplanar(const std::vector<Kernel::V3D> &vertices) {
if (!CoplanarChecks::sufficientPoints(vertices))
return false;
Kernel::V3D normal = CoplanarChecks::surfaceNormal(vertices);
// Check that a valid normal was found amongst collection of vertices
if (normal.norm2() == 0) {
// If all points are colinear. Not a plane.
return false;
}
return CoplanarChecks::allCoplanar(vertices, normal);
}
/// Returns signed 2 theta (signed scattering angle w.r.t. to beam direction).
double DetectorInfo::signedTwoTheta(const size_t index) const {
const Kernel::V3D samplePos = samplePosition();
const Kernel::V3D beamLine = samplePos - sourcePosition();
if (beamLine.nullVector()) {
throw Kernel::Exception::InstrumentDefinitionError(
"Source and sample are at same position!");
}
// Get the instrument up axis.
const Kernel::V3D &instrumentUpAxis =
m_instrument->getReferenceFrame()->vecPointingUp();
return getDetector(index)
.getSignedTwoTheta(samplePos, beamLine, instrumentUpAxis);
}
/**
* Find maximum angular half width of the bounding box from the observer, that
* is
* the greatest angle between the centre point and any corner point
* @param observer :: Viewing point
* @returns The value of the angular half-width
*/
double BoundingBox::angularWidth(const Kernel::V3D &observer) const {
Kernel::V3D centre = centrePoint() - observer;
std::vector<Kernel::V3D> pts;
this->getFullBox(pts, observer);
std::vector<Kernel::V3D>::const_iterator ip;
double centre_norm_inv = 1.0 / centre.norm();
double thetaMax(-1.0);
for (ip = pts.begin(); ip != pts.end(); ++ip) {
double theta = acos(ip->scalar_prod(centre) * centre_norm_inv / ip->norm());
if (theta > thetaMax)
thetaMax = theta;
}
return thetaMax;
}
/**
* Determines wither point is on the surface.
* @param point :: Point to check
* @returns true if the point is on the surface
*/
bool MeshObject::isOnSide(const Kernel::V3D &point) const {
BoundingBox bb = getBoundingBox();
if (!bb.isPointInside(point)) {
return false;
}
const std::vector<Kernel::V3D> directions = {
Kernel::V3D{0, 0, 1}, Kernel::V3D{0, 1, 0},
Kernel::V3D{1, 0, 0}}; // directions to look for intersections
// We have to look in several directions in case a point is on a face
// or edge parallel to the first direction or also the second direction.
for (const auto &direction : directions) {
std::vector<Kernel::V3D> intersectionPoints;
std::vector<TrackDirection> entryExitFlags;
getIntersections(point, direction, intersectionPoints, entryExitFlags);
if (intersectionPoints.empty()) {
return false;
}
for (const auto &intersectionPoint : intersectionPoints) {
if (point.distance(intersectionPoint) < M_TOLERANCE) {
return true;
}
}
}
return false;
}
double Cylinder::distance(const Kernel::V3D &A) const
/**
Calculates the distance of point A from
the surface of the cylinder.
@param A :: Point to calculate distance from
@return :: +ve distance to the surface.
\todo INCOMPLETE AS Does not deal with the case of
non axis centre line (has been updated?? )
*/
{
// First find the normal going to the point
const Kernel::V3D Amov = A - Centre;
double lambda = Amov.scalar_prod(Normal);
const Kernel::V3D Ccut = Normal * lambda;
// The distance is from the centre line to the
return fabs(Ccut.distance(Amov) - Radius);
}
/**
* Set the new detector position given the r,theta and phi.
* @param det :: A pointer to the detector
* @param l2 :: A single l2
* @param theta :: A single theta
* @param phi :: A single phi
*/
void UpdateInstrumentFromFile::setDetectorPosition(const Geometry::IDetector_const_sptr & det, const float l2,
const float theta, const float phi)
{
if( m_ignoreMonitors && det->isMonitor() ) return;
Geometry::ParameterMap & pmap = m_workspace->instrumentParameters();
Kernel::V3D pos;
if (!m_ignorePhi)
{
pos.spherical(l2, theta, phi);
}
else
{
double r,t,p;
det->getPos().getSpherical(r,t,p);
pos.spherical(l2, theta, p);
}
Geometry::ComponentHelper::moveComponent(*det, pmap, pos, Geometry::ComponentHelper::Absolute);
}
std::pair<double, double> LoadILLSANS::calculateQMaxQMin() {
double min = std::numeric_limits<double>::max(),
max = std::numeric_limits<double>::min();
g_log.debug("Calculating Qmin Qmax...");
std::size_t nHist = m_localWorkspace->getNumberHistograms();
for (std::size_t i = 0; i < nHist; ++i) {
Geometry::IDetector_const_sptr det = m_localWorkspace->getDetector(i);
if (!det->isMonitor()) {
const MantidVec &lambdaBinning = m_localWorkspace->readX(i);
Kernel::V3D detPos = det->getPos();
double r, theta, phi;
detPos.getSpherical(r, theta, phi);
double v1 = calculateQ(*(lambdaBinning.begin()), theta);
double v2 = calculateQ(*(lambdaBinning.end() - 1), theta);
// std::cout << "i=" << i << " theta="<<theta << " lambda_i=" <<
// *(lambdaBinning.begin()) << " lambda_f=" << *(lambdaBinning.end()-1) <<
// " v1=" << v1 << " v2=" << v2 << '\n';
if (i == 0) {
min = v1;
max = v1;
}
if (v1 < min) {
min = v1;
}
if (v2 < min) {
min = v2;
}
if (v1 > max) {
max = v1;
}
if (v2 > max) {
max = v2;
}
} else
g_log.debug() << "Detector " << i << " is a Monitor : " << det->getID()
<< '\n';
}
g_log.debug() << "Calculating Qmin Qmax. Done : [" << min << "," << max
<< "]\n";
return std::pair<double, double>(min, max);
}
double
Torus::distance(const Kernel::V3D& Pt) const
/**
Calculates the distance from the point to the Torus
does not calculate the point on the Torusthat is closest
@param Pt :: Point to calcuate from
- normalise to a cone vertex at the origin
- calculate the angle between the axis and the Point
- Calculate the distance to P
@return distance to Pt
*/
{
const Kernel::V3D Px=Pt-Centre;
// test is the centre to point distance is zero
if(Px.norm()<Tolerance)
return Px.norm();
return Px.norm();
}
double Plane::distance(const Kernel::V3D &A) const
/**
Determine the distance of point A from the plane
returns a value relative to the normal
@param A :: point to get distance from
@return singed distance from point
*/
{
return A.scalar_prod(NormV) - Dist;
}
int Line::intersect(std::list<Kernel::V3D> &PntOut, const Cylinder &Cyl) const
/**
For the line that intersects the cylinder generate
add the point to the VecOut, return number of points
added. It does not check the points for validity.
@param PntOut :: Vector of points found by the line/cylinder intersection
@param Cyl :: Cylinder to intersect line with
@return Number of points found by intersection
*/
{
const Kernel::V3D Cent = Cyl.getCentre();
const Kernel::V3D Ax = Origin - Cent;
const Kernel::V3D N = Cyl.getNormal();
const double R = Cyl.getRadius();
const double vDn = N.scalar_prod(Direct);
const double vDA = N.scalar_prod(Ax);
// First solve the equation of intersection
double C[3];
C[0] = 1.0 - (vDn * vDn);
C[1] = 2.0 * (Ax.scalar_prod(Direct) - vDA * vDn);
C[2] = Ax.scalar_prod(Ax) - (R * R + vDA * vDA);
std::pair<std::complex<double>, std::complex<double>> SQ;
const int ix = solveQuadratic(C, SQ);
// This takes the centre displacement into account:
return lambdaPair(ix, SQ, PntOut);
}
double Cone::distance(const Kernel::V3D& Pt) const
/**
Calculates the distance from the point to the Cone
does not calculate the point on the cone that is closest
@param Pt :: Point to calcuate from
- normalise to a cone vertex at the origin
- calculate the angle between the axis and the Point
- Calculate the distance to P
@return distance to Pt
*/
{
const Kernel::V3D Px = Pt - Centre;
// test is the centre to point distance is zero
if (Px.norm() < Tolerance)
return Px.norm();
double Pangle = Px.scalar_prod(Normal) / Px.norm();
if (Pangle < 0.0)
Pangle = acos(-Pangle);
else
Pangle = acos(Pangle);
Pangle -= M_PI * alpha / 180.0;
return Px.norm() * sin(Pangle);
}
/**
* This function calculates the exponential contribution to the He3 tube
* efficiency.
* @param spectraIndex :: the current index to calculate
* @param idet :: the current detector pointer
* @throw out_of_range if twice tube thickness is greater than tube diameter
* @return the exponential contribution for the given detector
*/
double He3TubeEfficiency::calculateExponential(
std::size_t spectraIndex,
boost::shared_ptr<const Geometry::IDetector> idet) {
// Get the parameters for the current associated tube
double pressure =
this->getParameter("TubePressure", spectraIndex, "tube_pressure", idet);
double tubethickness =
this->getParameter("TubeThickness", spectraIndex, "tube_thickness", idet);
double temperature = this->getParameter("TubeTemperature", spectraIndex,
"tube_temperature", idet);
double detRadius(0.0);
Kernel::V3D detAxis;
this->getDetectorGeometry(idet, detRadius, detAxis);
double detDiameter = 2.0 * detRadius;
double twiceTubeThickness = 2.0 * tubethickness;
// now get the sin of the angle, it's the magnitude of the cross product of
// unit vector along the detector tube axis and a unit vector directed from
// the sample to the detector center
Kernel::V3D vectorFromSample = idet->getPos() - this->samplePos;
vectorFromSample.normalize();
Kernel::Quat rot = idet->getRotation();
// rotate the original cylinder object axis to get the detector axis in the
// actual instrument
rot.rotate(detAxis);
detAxis.normalize();
// Scalar product is quicker than cross product
double cosTheta = detAxis.scalar_prod(vectorFromSample);
double sinTheta = std::sqrt(1.0 - cosTheta * cosTheta);
const double straight_path = detDiameter - twiceTubeThickness;
if (std::fabs(straight_path - 0.0) < TOL) {
throw std::out_of_range("Twice tube thickness cannot be greater than "
"or equal to the tube diameter");
}
const double pathlength = straight_path / sinTheta;
return EXP_SCALAR_CONST * (pressure / temperature) * pathlength;
}
void Cone::setNorm(const Kernel::V3D &A)
/**
Sets the Normal and the Base Equation
@param A :: New Normal direction
*/
{
if (A.norm() > Tolerance) {
Normal = A;
Normal.normalize();
setBaseEqn();
}
return;
}
int Line::intersect(std::list<Kernel::V3D> &PntOut, const Sphere &Sph) const
/**
For the line that intersects the cylinder generate
add the point to the VecOut, return number of points
added. It does not check the points for validity.
@param PntOut :: Vector of points found by the line/sphere intersection
@param Sph :: Sphere to intersect line with
@return Number of points found by intersection
*/
{
// Nasty stripping of useful stuff from sphere
const Kernel::V3D Ax = Origin - Sph.getCentre();
const double R = Sph.getRadius();
// First solve the equation of intersection
double C[3];
C[0] = 1;
C[1] = 2.0 * Ax.scalar_prod(Direct);
C[2] = Ax.scalar_prod(Ax) - R * R;
std::pair<std::complex<double>, std::complex<double>> SQ;
const int ix = solveQuadratic(C, SQ);
return lambdaPair(ix, SQ, PntOut);
}
/**
* Calculate volume.
* @return The volume.
*/
double MeshObject::volume() const {
// Select centre of bounding box as centre point.
// For each triangle calculate the signed volume of
// the tetrahedron formed by the triangle and the
// centre point. Then add to total.
BoundingBox bb = getBoundingBox();
double cX = 0.5 * (bb.xMax() + bb.xMin());
double cY = 0.5 * (bb.yMax() + bb.yMin());
double cZ = 0.5 * (bb.zMax() + bb.zMin());
Kernel::V3D centre(cX, cY, cZ);
double volumeTimesSix(0.0);
Kernel::V3D vertex1, vertex2, vertex3;
for (size_t i = 0; getTriangle(i, vertex1, vertex2, vertex3); ++i) {
Kernel::V3D a = vertex1 - centre;
Kernel::V3D b = vertex2 - centre;
Kernel::V3D c = vertex3 - centre;
volumeTimesSix += a.scalar_prod(b.cross_prod(c));
}
return volumeTimesSix / 6.0;
}
int Line::setLine(const Kernel::V3D &O, const Kernel::V3D &D)
/**
sets the line given the Origne and direction
@param O :: origin
@param D :: direction
@retval 0 :: Direction == 0 ie no line
@retval 1 :: on success
*/
{
if (D.nullVector())
return 0;
Origin = O;
Direct = D;
Direct.normalize();
return 1;
}
int Plane::setPlane(const Kernel::V3D &P, const Kernel::V3D &N)
/**
Given a point and a normal direction set the plane
@param P :: Point for plane to pass thought
@param N :: Normal for the plane
@retval 0 :: success
*/
{
try {
NormV = normalize(N);
} catch (std::runtime_error &) {
throw std::invalid_argument("Attempt to create Plane with zero normal");
}
Dist = P.scalar_prod(NormV);
setBaseEqn();
return 0;
}
/**
* Returns whether the given reflection is allowed or not in this space group
*
* Space groups that contain translational symmetry cause certain reflections
* to be absent due to the contributions of symmetry equivalent atoms to the
* structure factor cancelling out. This method implements the procedure
* described in ITA [1] to check whether a reflection is allowed or not
* according to the symmetry operations in the space group. Please note that
* certain arrangements of atoms can lead to additional conditions that can not
* be determined using a space group's symmetry operations alone. For these
* situations, Geometry::CrystalStructure can help.
*
* [1] International Tables for Crystallography (2006). Vol. A, ch. 12.3, p. 832
*
* @param hkl :: HKL to be checked.
* @return :: true if the reflection is allowed, false otherwise.
*/
bool SpaceGroup::isAllowedReflection(const Kernel::V3D &hkl) const {
for (const auto &operation : m_allOperations) {
if (operation.hasTranslation()) {
/* Floating point precision problem:
* (H . v) % 1.0 is not always exactly 0, so instead:
* | [(H . v) + delta] % 1.0 | > 1e-14 is checked
* The transformation is only performed if necessary.
*/
if ((fabs(fmod(fabs(hkl.scalar_prod(operation.reducedVector())) + 1e-15,
1.0)) > 1e-14) &&
(operation.transformHKL(hkl) == hkl)) {
return false;
}
}
}
return true;
}
/**
* Establish if all vertices are coplanar
* @param vertices : All vertices to check
* @param normal : Surface normal
* @return True only if all vertices are coplanar
*/
bool allCoplanar(const std::vector<Kernel::V3D> &vertices,
const Kernel::V3D &normal) {
bool in_plane = true;
auto v0 = vertices[0];
const auto nx = normal[0];
const auto ny = normal[1];
const auto nz = normal[2];
const auto k = nx * v0.X() + ny * v0.Y() + nz * v0.Z();
const auto denom = normal.norm();
const static double tolerance =
1e-9; // Fixed Tolerance. Too expensive to calculate
// based on machine uncertaintly for each
// vertex.
for (const auto &vertex : vertices) {
auto d = (nx * vertex.X() + ny * vertex.Y() + nz * vertex.Z() - k) / denom;
if (d > tolerance || d < -1 * tolerance) {
in_plane = false;
break;
}
}
return in_plane;
}
/**
* Return a local point in a cylinder shape
*
* @param basis a basis vector
* @param alongAxis symmetry axis vector of a cylinder
* @param polarAngle a polar angle (in radians) of a point in a cylinder
* @param radialLength radial position of point in a cylinder
* @return a local point inside the cylinder
*/
Kernel::V3D localPointInCylinder(const Kernel::V3D &basis,
const Kernel::V3D &alongAxis,
double polarAngle, double radialLength) {
// Use basis to get a second perpendicular vector to define basis2
Kernel::V3D basis2;
if (basis.X() == 0) {
basis2.setX(1.);
} else if (basis.Y() == 0) {
basis2.setY(1.);
} else if (basis.Z() == 0) {
basis2.setZ(1.);
} else {
basis2.setX(-basis.Y());
basis2.setY(basis.X());
basis2.normalize();
}
const Kernel::V3D basis3{basis.cross_prod(basis2)};
const Kernel::V3D localPoint{
((basis2 * std::cos(polarAngle) + basis3 * std::sin(polarAngle)) *
radialLength) +
alongAxis};
return localPoint;
}