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CoordTransformAffine.cpp
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CoordTransformAffine.cpp
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// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
// NScD Oak Ridge National Laboratory, European Spallation Source,
// Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidDataObjects/CoordTransformAffine.h"
#include "MantidAPI/CoordTransform.h"
#include "MantidDataObjects/CoordTransformAligned.h"
#include "MantidGeometry/MDGeometry/MDTypes.h"
#include "MantidKernel/Exception.h"
#include "MantidKernel/Matrix.h"
#include "MantidKernel/System.h"
#include "MantidKernel/VectorHelper.h"
#include <boost/algorithm/string.hpp>
#include <boost/format.hpp>
using namespace Mantid::Geometry;
using namespace Mantid::Kernel;
using Mantid::API::CoordTransform;
namespace Mantid {
namespace DataObjects {
//----------------------------------------------------------------------------------------------
/** Constructor.
* Construct the affine matrix to and initialize to an identity matrix.
* @param inD :: input number of dimensions, >= 1
* @param outD :: output number of dimensions, <= inD
* @throw std::runtime_error if outD > inD
*/
CoordTransformAffine::CoordTransformAffine(const size_t inD, const size_t outD)
: CoordTransform(inD, outD), m_affineMatrix(outD + 1, inD + 1), m_rawMatrix(nullptr), m_rawMemory(nullptr) {
m_affineMatrix.identityMatrix();
// Allocate the raw matrix
size_t nx = m_affineMatrix.numRows();
size_t ny = m_affineMatrix.numCols();
// vector of pointers
m_rawMatrix = new coord_t *[nx];
// memory itself
m_rawMemory = new coord_t[nx * ny];
for (size_t i = 0; i < nx; i++)
m_rawMatrix[i] = m_rawMemory + (i * ny);
// Copy into the raw matrix (for speed)
copyRawMatrix();
}
//----------------------------------------------------------------------------------------------
/** Destructor
*/
CoordTransformAffine::~CoordTransformAffine() {
// delete array of pointers to rows
delete[] m_rawMatrix;
m_rawMatrix = nullptr;
// delete large mem block holding the matrix
delete[] m_rawMemory;
m_rawMemory = nullptr;
}
//----------------------------------------------------------------------------------------------
/** Copies the affine matrix into a local raw pointer, for speed.
* Call this after any change to affineMatrix
*/
void CoordTransformAffine::copyRawMatrix() {
for (size_t x = 0; x < m_affineMatrix.numRows(); ++x)
for (size_t y = 0; y < m_affineMatrix.numCols(); ++y)
m_rawMatrix[x][y] = m_affineMatrix[x][y];
}
//----------------------------------------------------------------------------------------------
/** Virtual cloner
* @return a copy of this object */
CoordTransform *CoordTransformAffine::clone() const {
auto out = new CoordTransformAffine(inD, outD);
out->setMatrix(this->getMatrix());
return out;
}
//----------------------------------------------------------------------------------------------
/** Directly set the affine matrix to use.
*
* @param newMatrix :: (outD+1 * inD+1) matrix to set.
* @throw runtime_error if the matrix dimensions are incompatible.
*/
void CoordTransformAffine::setMatrix(const Mantid::Kernel::Matrix<coord_t> &newMatrix) {
if (newMatrix.numRows() != outD + 1)
throw std::runtime_error("setMatrix(): Number of rows must match!");
if (newMatrix.numCols() != inD + 1)
throw std::runtime_error("setMatrix(): Number of columns must match!");
m_affineMatrix = newMatrix;
// Copy into the raw matrix (for speed)
copyRawMatrix();
}
//----------------------------------------------------------------------------------------------
/** Return the affine matrix in the transform.
*/
const Mantid::Kernel::Matrix<coord_t> &CoordTransformAffine::getMatrix() const { return m_affineMatrix; }
/** @return the affine matrix */
Mantid::Kernel::Matrix<coord_t> CoordTransformAffine::makeAffineMatrix() const { return m_affineMatrix; }
//----------------------------------------------------------------------------------------------
/** Add a translation (in the output coordinates) to the transform.
*
* @param translationVector :: fixed-size array of the translation vector, of
*size outD
*/
void CoordTransformAffine::addTranslation(const coord_t *translationVector) {
Matrix<coord_t> translationMatrix(outD + 1, inD + 1);
// Start with identity
translationMatrix.identityMatrix();
// Fill the last column with the translation value
for (size_t i = 0; i < outD; i++)
translationMatrix[i][inD] = translationVector[i];
// Multiply the affine matrix by the translation affine matrix to combine them
m_affineMatrix *= translationMatrix;
// Copy into the raw matrix (for speed)
copyRawMatrix();
}
//----------------------------------------------------------------------------------------------
/** 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
m_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++)
m_affineMatrix[i][j] = static_cast<coord_t>(basis[j] * scaling[i]);
// Now account for the translation
coord_t transl = 0;
for (size_t j = 0; j < basis.size(); j++)
transl += static_cast<coord_t>(origin[j] * basis[j]); // dot product of origin * basis aka ( X0 . U )
// The last column of the matrix = the translation movement
m_affineMatrix[i][inD] = -transl * static_cast<coord_t>(scaling[i]);
}
// Copy into the raw matrix (for speed)
copyRawMatrix();
}
void CoordTransformAffine::buildNonOrthogonal(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::buildNonOrthogonal(): the "
"origin must be in the dimensions of the input "
"workspace (length inD).");
if (axes.size() != outD)
throw std::runtime_error("CoordTransformAffine::buildNonOrthogonal(): you "
"must give as many basis vectors as there are "
"dimensions in the output workspace.");
if (scaling.size() != outD)
throw std::runtime_error("CoordTransformAffine::buildNonOrthogonal(): the "
"size of the scaling vector must be the same as "
"the number of dimensions in the output "
"workspace.");
// Start with identity
m_affineMatrix.identityMatrix();
// A matrix is columns of basis vectors
Mantid::Kernel::Matrix<coord_t> A(inD, outD);
for (size_t i = 0; i < outD; i++) {
for (size_t j = 0; j < inD; j++) {
A[j][i] = axes[i][j];
}
}
Mantid::Kernel::Matrix<coord_t> AT = A;
AT.Transpose();
Mantid::Kernel::Matrix<coord_t> ATA = AT * A;
ATA.Invert();
Mantid::Kernel::Matrix<coord_t> Ainv = ATA * AT;
Mantid::Kernel::Matrix<coord_t> offset(inD, 1);
for (size_t j = 0; j < inD; j++) {
offset[j][0] = origin[j];
}
Mantid::Kernel::Matrix<coord_t> outoffset = Ainv * offset;
for (size_t i = 0; i < outD; i++) {
for (size_t j = 0; j < inD; j++) {
m_affineMatrix[i][j] = Ainv[i][j] * scaling[i];
}
m_affineMatrix[i][inD] = -outoffset[i][0] * scaling[i];
}
// Copy into the raw matrix (for speed)
copyRawMatrix();
}
//----------------------------------------------------------------------------------------------
/** Apply the coordinate transformation
*
* @param inputVector :: fixed-size array of input coordinates, of size inD
* @param outVector :: fixed-size array of output coordinates, of size outD
*/
void CoordTransformAffine::apply(const coord_t *inputVector, coord_t *outVector) const {
// For each output dimension
for (size_t out = 0; out < outD; ++out) {
// Cache the row pointer to make the matrix access a bit faster
coord_t *rawMatrixRow = m_rawMatrix[out];
coord_t outVal = 0.0;
size_t in;
for (in = 0; in < inD; ++in)
outVal += rawMatrixRow[in] * inputVector[in];
// The last input coordinate is "1" always (made homogenous coordinate out
// of the input x,y,etc.)
outVal += rawMatrixRow[in];
// Save in the output
outVector[out] = outVal;
}
}
//----------------------------------------------------------------------------------------------
/** Serialize the coordinate transform
*
* @return The coordinate transform in its serialized form.
*/
std::string CoordTransformAffine::toXMLString() const {
using namespace Poco::XML;
AutoPtr<Document> pDoc = new Document;
AutoPtr<Element> coordTransformElement = pDoc->createElement("CoordTransform");
pDoc->appendChild(coordTransformElement);
AutoPtr<Element> coordTransformTypeElement = pDoc->createElement("Type");
coordTransformTypeElement->appendChild(AutoPtr<Node>(pDoc->createTextNode("CoordTransformAffine")));
coordTransformElement->appendChild(coordTransformTypeElement);
AutoPtr<Element> paramListElement = pDoc->createElement("ParameterList");
AutoPtr<Text> formatText = pDoc->createTextNode("%s%s%s");
paramListElement->appendChild(formatText);
coordTransformElement->appendChild(paramListElement);
std::stringstream xmlstream;
DOMWriter writer;
writer.writeNode(xmlstream, pDoc);
// Convert the members to parameters
AffineMatrixParameter affineMatrixParameter(inD, outD);
affineMatrixParameter.setMatrix(m_affineMatrix);
Mantid::API::InDimParameter inD_param(inD);
Mantid::API::OutDimParameter outD_param(outD);
std::string formattedXMLString =
boost::str(boost::format(xmlstream.str().c_str()) % inD_param.toXMLString().c_str() %
outD_param.toXMLString().c_str() % affineMatrixParameter.toXMLString().c_str());
return formattedXMLString;
}
/**
* Coordinate transform id
* @return the type of coordinate transform
*/
std::string CoordTransformAffine::id() const { return "CoordTransformAffine"; }
//----------------------------------------------------------------------------------------------
/** Combine two transformations into a single affine transformations
*
* @param first :: CoordTransformAffine or CoordTransformAligned transform.
* @param second :: CoordTransformAffine or CoordTransformAligned transform.
* @return pointer to a new CoordTransformAffine combining both
* @throw std::runtime_error if one of the inputs is not CoordTransformAffine or
*CoordTransformAligned
*/
CoordTransformAffine *CoordTransformAffine::combineTransformations(CoordTransform *first, CoordTransform *second) {
if (!first || !second)
throw std::runtime_error("CoordTransformAffine::combineTransformations(): Null input provided.");
if (second->getInD() != first->getOutD())
throw std::runtime_error("CoordTransformAffine::combineTransformations(): "
"The # of output dimensions of first must be the "
"same as the # of input dimensions of second.");
// Convert both inputs to affine matrices, if needed
auto *firstAff = dynamic_cast<CoordTransformAffine *>(first);
bool ownFirstAff(false);
if (!firstAff) {
auto *firstAl = dynamic_cast<CoordTransformAligned *>(first);
if (!firstAl)
throw std::runtime_error("CoordTransformAffine::combineTransformations(): first transform "
"must be either CoordTransformAffine or CoordTransformAligned.");
firstAff = new CoordTransformAffine(firstAl->getInD(), firstAl->getOutD());
firstAff->setMatrix(firstAl->makeAffineMatrix());
ownFirstAff = true;
}
auto *secondAff = dynamic_cast<CoordTransformAffine *>(second);
bool ownSecondAff(false);
if (!secondAff) {
auto *secondAl = dynamic_cast<CoordTransformAligned *>(second);
if (!secondAl)
throw std::runtime_error("CoordTransformAffine::combineTransformations(): second transform "
"must be either CoordTransformAffine or CoordTransformAligned.");
secondAff = new CoordTransformAffine(secondAl->getInD(), secondAl->getOutD());
secondAff->setMatrix(secondAl->makeAffineMatrix());
ownSecondAff = true;
}
// Initialize the affine matrix
auto out = new CoordTransformAffine(firstAff->getInD(), secondAff->getOutD());
// Multiply the two matrices together
Matrix<coord_t> outMat = secondAff->getMatrix() * firstAff->getMatrix();
// Set in the output
out->setMatrix(outMat);
// Clean up
if (ownFirstAff)
delete firstAff;
if (ownSecondAff)
delete secondAff;
return out;
}
} // namespace DataObjects
} // namespace Mantid