/** Build a coordinate transformation based on an origin and orthogonal basis vectors.
* This can reduce the number of dimensions. For example:
*
* - The input position is X=(x,y,z)
* - The origin is X0=(x0,y0,z0)
* - The basis vectors are U and V (reducing from 3 to 2D)
* - The output position u = (X-X0).U = X.U - X0.U = x*Ux + y*Uy + z*Uz + (X0.U)
* - The output position v = (X-X0).V = X.V - X0.V = x*Vx + y*Vy + z*Vz + (X0.V)
*
* And this allows us to create the affine matrix:
*
* | Ux Uy Uz X0.U | | x | | u |
* | Vx Vy Vz X0.V | | y | = | v |
* | 0 0 0 1 | | z | | 1 |
* | 1 |
*
* @param origin :: origin (in the inDimension), which corresponds to (0,0,...) in outD
* @param axes :: a list of basis vectors. There must be outD vectors (one for each output dimension)
* and each vector must be of length inD (all coordinates in the input dimension).
* The vectors must be properly orthogonal: not coplanar or collinear. This is not checked!
* @param scaling :: a vector of size outD of the scaling to perform in each of the
* OUTPUT dimensions.
* @throw if inconsistent vector sizes are received, or zero-length
*/
void CoordTransformAffine::buildOrthogonal(const Mantid::Kernel::VMD & origin, const std::vector< Mantid::Kernel::VMD> & axes,
const Mantid::Kernel::VMD & scaling)
{
if (origin.size() != inD)
throw std::runtime_error("CoordTransformAffine::buildOrthogonal(): the origin must be in the dimensions of the input workspace (length inD).");
if (axes.size() != outD)
throw std::runtime_error("CoordTransformAffine::buildOrthogonal(): you must give as many basis vectors as there are dimensions in the output workspace.");
if (scaling.size() != outD)
throw std::runtime_error("CoordTransformAffine::buildOrthogonal(): the size of the scaling vector must be the same as the number of dimensions in the output workspace.");
// Start with identity
affineMatrix.identityMatrix();
for (size_t i=0; i<axes.size(); i++)
{
if (axes[i].length() == 0.0)
throw std::runtime_error("CoordTransformAffine::buildOrthogonal(): one of the basis vector was of zero length.");
if (axes[i].size() != inD)
throw std::runtime_error("CoordTransformAffine::buildOrthogonal(): one of the basis vectors had the wrong number of dimensions (must be inD).");
// Normalize each axis to unity
VMD basis = axes[i];
basis.normalize();
// The row of the affine matrix = the unit vector
for (size_t j=0; j<basis.size(); j++)
affineMatrix[i][j] = basis[j] * scaling[i];
// Now account for the translation
coord_t transl = 0;
for (size_t j=0; j<basis.size(); j++)
transl += origin[j] * basis[j]; // dot product of origin * basis aka ( X0 . U )
// The last column of the matrix = the translation movement
affineMatrix[i][inD] = -transl * scaling[i];
}
// Copy into the raw matrix (for speed)
copyRawMatrix();
}
/** Obtain coordinates for a line plot through a MDWorkspace.
* Cross the workspace from start to end points, recording the signal along the
*lin at either bin boundaries, or halfway between bin boundaries (which is bin
*centres if the line is dimension aligned). If recording halfway values then
*omit points in masked bins.
*
* @param start :: coordinates of the start point of the line
* @param end :: coordinates of the end point of the line
* @param normalize :: how to normalize the signal
* @returns :: LinePlot with x as the boundaries of the bins, relative
* to start of the line, y set to the normalized signal for each bin with
* Length = length(x) - 1 and e as the error vector for each bin.
* @param bin_centres :: if true then record points halfway between bin
*boundaries, otherwise record on bin boundaries
*/
IMDWorkspace::LinePlot MDHistoWorkspace::getLinePoints(
const Mantid::Kernel::VMD &start, const Mantid::Kernel::VMD &end,
Mantid::API::MDNormalization normalize, const bool bin_centres) const {
LinePlot line;
size_t nd = this->getNumDims();
if (start.getNumDims() != nd)
throw std::runtime_error("Start point must have the same number of "
"dimensions as the workspace.");
if (end.getNumDims() != nd)
throw std::runtime_error(
"End point must have the same number of dimensions as the workspace.");
// Unit-vector of the direction
VMD dir = end - start;
const auto length = dir.normalize();
// Vector with +1 where direction is positive, -1 where negative
#define sgn(x) ((x < 0) ? -1.0f : ((x > 0.) ? 1.0f : 0.0f))
VMD dirSign(nd);
for (size_t d = 0; d < nd; d++) {
dirSign[d] = sgn(dir[d]);
}
const size_t BADINDEX = size_t(-1);
// Dimensions of the workspace
boost::scoped_array<size_t> index(new size_t[nd]);
boost::scoped_array<size_t> numBins(new size_t[nd]);
for (size_t d = 0; d < nd; d++) {
IMDDimension_const_sptr dim = this->getDimension(d);
index[d] = BADINDEX;
numBins[d] = dim->getNBins();
}
const std::set<coord_t> boundaries =
getBinBoundariesOnLine(start, end, nd, dir, length);
if (boundaries.empty()) {
this->makeSinglePointWithNaN(line.x, line.y, line.e);
// Require x.size() = y.size()+1 if recording bin boundaries
if (!bin_centres)
line.x.push_back(length);
return line;
} else {
// Get the first point
std::set<coord_t>::iterator it;
it = boundaries.cbegin();
coord_t lastLinePos = *it;
VMD lastPos = start + (dir * lastLinePos);
if (!bin_centres) {
line.x.push_back(lastLinePos);
}
++it;
coord_t linePos = 0;
for (; it != boundaries.cend(); ++it) {
// This is our current position along the line
linePos = *it;
// This is the full position at this boundary
VMD pos = start + (dir * linePos);
// Position in the middle of the bin
VMD middle = (pos + lastPos) * 0.5;
// Find the signal in this bin
const auto linearIndex =
this->getLinearIndexAtCoord(middle.getBareArray());
if (bin_centres && !this->getIsMaskedAt(linearIndex)) {
coord_t bin_centrePos =
static_cast<coord_t>((linePos + lastLinePos) * 0.5);
line.x.push_back(bin_centrePos);
} else if (!bin_centres)
line.x.push_back(linePos);
if (linearIndex < m_length) {
auto normalizer = getNormalizationFactor(normalize, linearIndex);
// And add the normalized signal/error to the list too
auto signal = this->getSignalAt(linearIndex) * normalizer;
if (boost::math::isinf(signal)) {
// The plotting library (qwt) doesn't like infs.
signal = std::numeric_limits<signal_t>::quiet_NaN();
}
if (!bin_centres || !this->getIsMaskedAt(linearIndex)) {
line.y.push_back(signal);
line.e.push_back(this->getErrorAt(linearIndex) * normalizer);
}
// Save the position for next bin
lastPos = pos;
} else {
// Invalid index. This shouldn't happen
line.y.push_back(std::numeric_limits<signal_t>::quiet_NaN());
line.e.push_back(std::numeric_limits<signal_t>::quiet_NaN());
}
lastLinePos = linePos;
} // for each unique boundary
// If all bins were masked
if (line.x.size() == 0) {
this->makeSinglePointWithNaN(line.x, line.y, line.e);
}
}
return line;
}