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SetSample.cpp
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SetSample.cpp
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#include "MantidDataHandling/SetSample.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/Sample.h"
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/Goniometer.h"
#include "MantidGeometry/Instrument/ReferenceFrame.h"
#include "MantidGeometry/Instrument/SampleEnvironmentFactory.h"
#include "MantidKernel/ConfigService.h"
#include "MantidKernel/FacilityInfo.h"
#include "MantidKernel/InstrumentInfo.h"
#include "MantidKernel/Logger.h"
#include "MantidKernel/Material.h"
#include "MantidKernel/Matrix.h"
#include "MantidKernel/PropertyManager.h"
#include "MantidKernel/PropertyManagerProperty.h"
#include <boost/algorithm/string/case_conv.hpp>
#include <boost/algorithm/string/predicate.hpp>
#include <Poco/Path.h>
namespace Mantid {
namespace DataHandling {
using Geometry::Goniometer;
using Geometry::ReferenceFrame;
using Geometry::SampleEnvironment;
using Kernel::Logger;
using Kernel::PropertyWithValue;
using Kernel::Quat;
using Kernel::V3D;
namespace {
/// Private namespace storing property name strings
namespace PropertyNames {
/// Input workspace property name
const std::string INPUT_WORKSPACE("InputWorkspace");
/// Geometry property name
const std::string GEOMETRY("Geometry");
/// Material property name
const std::string MATERIAL("Material");
/// Environment property name
const std::string ENVIRONMENT("Environment");
}
/// Private namespace storing sample environment args
namespace SEArgs {
/// Static Name string
const std::string NAME("Name");
/// Static Container string
const std::string CONTAINER("Container");
}
/// Provate namespace storing geometry args
namespace GeometryArgs {
/// Static Shape string
const std::string SHAPE("Shape");
}
/// Private namespace storing sample environment args
namespace ShapeArgs {
/// Static FlatPlate string
const std::string FLAT_PLATE("FlatPlate");
/// Static Cylinder string
const std::string CYLINDER("Cylinder");
/// Static HollowCylinder string
const std::string HOLLOW_CYLINDER("HollowCylinder");
/// Static CSG string
const std::string CSG("CSG");
/// Static Width string
const std::string WIDTH("Width");
/// Static Height string
const std::string HEIGHT("Height");
/// Static Thick string
const std::string THICK("Thick");
/// Static Center string
const std::string CENTER("Center");
/// Static Radius string
const std::string RADIUS("Radius");
/// Static InnerRadius string
const std::string INNER_RADIUS("InnerRadius");
/// Static OuterRadius string
const std::string OUTER_RADIUS("OuterRadius");
}
/**
* Return the centre coordinates of the base of a cylinder given the
* coordinates of the centre of the cylinder
* @param cylCentre Coordinates of centre of the cylinder (X,Y,Z) (in metres)
* @param height Height of the cylinder (in metres)
* @param axis The index of the height-axis of the cylinder
*/
V3D cylBaseCentre(const std::vector<double> &cylCentre, double height,
unsigned axisIdx) {
const V3D halfHeight = [&]() {
switch (axisIdx) {
case 0:
return V3D(0.5 * height, 0, 0);
case 1:
return V3D(0, 0.5 * height, 0);
case 2:
return V3D(0, 0, 0.5 * height);
default:
return V3D();
}
}();
return V3D(cylCentre[0], cylCentre[1], cylCentre[2]) - halfHeight;
}
/**
* Create the xml tag require for a given axis index
* @param axisIdx Index 0,1,2 for the axis of a cylinder
* @return A string containing the axis tag for this index
*/
std::string axisXML(unsigned axisIdx) {
switch (axisIdx) {
case 0:
return "<axis x=\"1\" y=\"0\" z=\"0\" />";
case 1:
return "<axis x=\"0\" y=\"1\" z=\"0\" />";
case 2:
return "<axis x=\"0\" y=\"0\" z=\"1\" />";
default:
return "";
}
}
}
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(SetSample)
/// Algorithms name for identification. @see Algorithm::name
const std::string SetSample::name() const { return "SetSample"; }
/// Algorithm's version for identification. @see Algorithm::version
int SetSample::version() const { return 1; }
/// Algorithm's category for identification. @see Algorithm::category
const std::string SetSample::category() const { return "Sample"; }
/// Algorithm's summary for use in the GUI and help. @see Algorithm::summary
const std::string SetSample::summary() const {
return "Set properties of the sample and its environment for a workspace";
}
/// Validate the inputs against each other @see Algorithm::validateInputs
std::map<std::string, std::string> SetSample::validateInputs() {
using Kernel::PropertyManager;
using Kernel::PropertyManager_const_sptr;
std::map<std::string, std::string> errors;
auto existsAndNotEmptyString =
[](const PropertyManager &pm, const std::string &name) {
if (pm.existsProperty(name)) {
const auto value = pm.getPropertyValue(name);
return !value.empty();
}
return false;
};
auto existsAndNegative =
[](const PropertyManager &pm, const std::string &name) {
if (pm.existsProperty(name)) {
const double value = pm.getProperty(name);
if (value < 0.0) {
return true;
}
}
return false;
};
// Validate Environment
const PropertyManager_const_sptr environArgs =
getProperty(PropertyNames::ENVIRONMENT);
if (environArgs) {
if (!existsAndNotEmptyString(*environArgs, SEArgs::NAME)) {
errors[PropertyNames::ENVIRONMENT] =
"Environment flags require a non-empty 'Name' entry.";
}
if (!existsAndNotEmptyString(*environArgs, SEArgs::CONTAINER)) {
errors[PropertyNames::ENVIRONMENT] =
"Environment flags require a non-empty 'Container' entry.";
}
}
// Validate as much of the shape information as possible
const PropertyManager_const_sptr geomArgs =
getProperty(PropertyNames::GEOMETRY);
if (geomArgs) {
if (existsAndNotEmptyString(*geomArgs, GeometryArgs::SHAPE)) {
const std::array<const std::string *, 6> positiveValues = {
{&ShapeArgs::HEIGHT, &ShapeArgs::WIDTH, &ShapeArgs::THICK,
&ShapeArgs::RADIUS, &ShapeArgs::INNER_RADIUS,
&ShapeArgs::OUTER_RADIUS}};
for (const auto &arg : positiveValues) {
if (existsAndNegative(*geomArgs, *arg)) {
errors[PropertyNames::GEOMETRY] = *arg + " argument < 0.0";
}
}
}
}
return errors;
}
/**
* Initialize the algorithm's properties.
*/
void SetSample::init() {
using API::WorkspaceProperty;
using Kernel::Direction;
using Kernel::PropertyManagerProperty;
// Inputs
declareProperty(Kernel::make_unique<WorkspaceProperty<>>(
PropertyNames::INPUT_WORKSPACE, "", Direction::InOut),
"A workspace whose sample properties will be updated");
declareProperty(Kernel::make_unique<PropertyManagerProperty>(
PropertyNames::GEOMETRY, Direction::Input),
"A dictionary of geometry parameters for the sample.");
declareProperty(Kernel::make_unique<PropertyManagerProperty>(
PropertyNames::MATERIAL, Direction::Input),
"A dictionary of material parameters for the sample. See "
"SetSampleMaterial for all accepted parameters");
declareProperty(
Kernel::make_unique<PropertyManagerProperty>(PropertyNames::ENVIRONMENT,
Direction::Input),
"A dictionary of parameters to configure the sample environment");
}
/**
* Execute the algorithm.
*/
void SetSample::exec() {
using API::MatrixWorkspace_sptr;
using Kernel::PropertyManager_sptr;
MatrixWorkspace_sptr workspace = getProperty(PropertyNames::INPUT_WORKSPACE);
PropertyManager_sptr environArgs = getProperty(PropertyNames::ENVIRONMENT);
PropertyManager_sptr geometryArgs = getProperty(PropertyNames::GEOMETRY);
PropertyManager_sptr materialArgs = getProperty(PropertyNames::MATERIAL);
// The order here is important. Se the environment first. If this
// defines a sample geometry then we can process the Geometry flags
// combined with this
const SampleEnvironment *sampleEnviron(nullptr);
if (environArgs) {
sampleEnviron = setSampleEnvironment(workspace, environArgs);
}
if (geometryArgs || sampleEnviron) {
setSampleShape(workspace, geometryArgs, sampleEnviron);
}
// Finally the material arguments
if (materialArgs) {
runChildAlgorithm("SetSampleMaterial", workspace, *materialArgs);
}
}
/**
* Set the requested sample environment on the workspace
* @param workspace A pointer to the workspace to be affected
* @param args The dictionary of flags for the environment
* @return A pointer to the new sample environment
*/
const Geometry::SampleEnvironment *SetSample::setSampleEnvironment(
API::MatrixWorkspace_sptr &workspace,
const Kernel::PropertyManager_const_sptr &args) {
using Geometry::SampleEnvironmentSpecFileFinder;
using Geometry::SampleEnvironmentFactory;
using Kernel::ConfigService;
const std::string envName = args->getPropertyValue(SEArgs::NAME);
const std::string canName = args->getPropertyValue(SEArgs::CONTAINER);
// The specifications need to be qualified by the facility and instrument.
// Check instrument for name and then lookup facility if facility
// is unknown then set to default facility & instrument.
auto instrument = workspace->getInstrument();
const auto &instOnWS = instrument->getName();
const auto &config = ConfigService::Instance();
std::string facilityName, instrumentName;
try {
const auto &instInfo = config.getInstrument(instOnWS);
instrumentName = instInfo.name();
facilityName = instInfo.facility().name();
} catch (std::runtime_error &) {
// use default facility/instrument
facilityName = config.getFacility().name();
instrumentName = config.getInstrument().name();
}
const auto &instDirs = config.getInstrumentDirectories();
std::vector<std::string> environDirs(instDirs);
for (auto &direc : environDirs) {
direc = Poco::Path(direc).append("sampleenvironments").toString();
}
auto finder =
Kernel::make_unique<SampleEnvironmentSpecFileFinder>(environDirs);
SampleEnvironmentFactory factory(std::move(finder));
auto sampleEnviron =
factory.create(facilityName, instrumentName, envName, canName);
workspace->mutableSample().setEnvironment(sampleEnviron.release());
return &(workspace->sample().getEnvironment());
}
/**
* @param workspace A pointer to the workspace to be affected
* @param args The user-supplied dictionary of flags
* @param sampleEnv A pointer to the sample environment if one exists, otherwise
* null
* @return A string containing the XML definition of the shape
*/
void SetSample::setSampleShape(API::MatrixWorkspace_sptr &workspace,
const Kernel::PropertyManager_const_sptr &args,
const Geometry::SampleEnvironment *sampleEnv) {
using Geometry::Container;
/* The sample geometry can be specified in two ways:
- a known set of primitive shapes with values or CSG string
- or a <samplegeometry> field sample environment can, with values possible
overridden by the Geometry flags
*/
// Try known shapes or CSG first if supplied
if (args) {
const auto refFrame = workspace->getInstrument()->getReferenceFrame();
const auto xml = tryCreateXMLFromArgsOnly(*args, *refFrame);
if (!xml.empty()) {
runSetSampleShape(workspace, xml);
return;
}
}
// Any arguments in the args dict are assumed to be values that should
// override the default set by the sampleEnv samplegeometry if it exists
if (sampleEnv) {
if (sampleEnv->container()->hasSampleShape()) {
const auto &can = sampleEnv->container();
Container::ShapeArgs shapeArgs;
if (args) {
const auto &props = args->getProperties();
for (const auto &prop : props) {
// assume in cm
const double val = args->getProperty(prop->name());
shapeArgs.emplace(boost::algorithm::to_lower_copy(prop->name()),
val * 0.01);
}
}
auto shapeObject = can->createSampleShape(shapeArgs);
// Set the object directly on the sample ensuring we preserve the
// material
const auto mat = workspace->sample().getMaterial();
shapeObject->setMaterial(mat);
workspace->mutableSample().setShape(*shapeObject);
} else {
throw std::runtime_error("The can does not define the sample shape. "
"Please either provide a 'Shape' argument "
"or update the environment definition with "
"this information.");
}
} else {
throw std::runtime_error("No sample environment defined, please provide "
"a 'Shape' argument to define the sample "
"shape.");
}
}
/**
* Create the required XML for a given shape type plus its arguments
* @param args A dict of flags defining the shape
* @param refFrame Defines the reference frame for the shape
* @return A string containing the XML if possible or an empty string
*/
std::string
SetSample::tryCreateXMLFromArgsOnly(const Kernel::PropertyManager &args,
const Geometry::ReferenceFrame &refFrame) {
std::string result;
if (!args.existsProperty(GeometryArgs::SHAPE)) {
return result;
}
const auto shape = args.getPropertyValue(GeometryArgs::SHAPE);
if (shape == ShapeArgs::CSG) {
result = args.getPropertyValue("Value");
} else if (shape == ShapeArgs::FLAT_PLATE) {
result = createFlatPlateXML(args, refFrame);
} else if (boost::algorithm::ends_with(shape, ShapeArgs::CYLINDER)) {
result = createCylinderLikeXML(
args, refFrame,
boost::algorithm::equals(shape, ShapeArgs::HOLLOW_CYLINDER));
} else {
throw std::invalid_argument(
"Unknown 'Shape' argument provided in "
"'Geometry'. Allowed "
"values=FlatPlate,CSG,Cylinder,HollowCylinder.");
}
if (g_log.is(Logger::Priority::PRIO_DEBUG)) {
g_log.debug("XML shape definition:\n" + result + '\n');
}
return result;
}
/**
* Create the XML required to define a flat plate from the given args
* @param args A user-supplied dict of args
* @param refFrame Defines the reference frame for the shape
* @return The XML definition string
*/
std::string
SetSample::createFlatPlateXML(const Kernel::PropertyManager &args,
const Geometry::ReferenceFrame &refFrame) const {
// Helper to take 3 coordinates and turn them to a V3D respecting the
// current reference frame
auto makeV3D = [&refFrame](double x, double y, double z) {
V3D v;
v[refFrame.pointingHorizontal()] = x;
v[refFrame.pointingUp()] = y;
v[refFrame.pointingAlongBeam()] = z;
return v;
};
const double widthInCM = args.getProperty(ShapeArgs::WIDTH);
const double heightInCM = args.getProperty(ShapeArgs::HEIGHT);
const double thickInCM = args.getProperty(ShapeArgs::THICK);
// Convert to half-"width" in metres
const double szX = (widthInCM * 5e-3);
const double szY = (heightInCM * 5e-3);
const double szZ = (thickInCM * 5e-3);
// Contruct cuboid corners. Define points about origin, rotate and then
// translate to final center position
auto lfb = makeV3D(szX, -szY, -szZ);
auto lft = makeV3D(szX, szY, -szZ);
auto lbb = makeV3D(szX, -szY, szZ);
auto rfb = makeV3D(-szX, -szY, -szZ);
// optional rotation about the center of object
if (args.existsProperty("Angle")) {
Goniometer gr;
const auto upAxis = makeV3D(0, 1, 0);
gr.pushAxis("up", upAxis.X(), upAxis.Y(), upAxis.Z(),
args.getProperty("Angle"), Geometry::CCW, Geometry::angDegrees);
auto &rotation = gr.getR();
lfb.rotate(rotation);
lft.rotate(rotation);
lbb.rotate(rotation);
rfb.rotate(rotation);
}
std::vector<double> center = args.getProperty(ShapeArgs::CENTER);
const V3D centrePos(center[0] * 0.01, center[1] * 0.01, center[2] * 0.01);
// translate to true center after rotation
lfb += centrePos;
lft += centrePos;
lbb += centrePos;
rfb += centrePos;
std::ostringstream xmlShapeStream;
xmlShapeStream << " <cuboid id=\"sample-shape\"> "
<< "<left-front-bottom-point x=\"" << lfb.X() << "\" y=\""
<< lfb.Y() << "\" z=\"" << lfb.Z() << "\" /> "
<< "<left-front-top-point x=\"" << lft.X() << "\" y=\""
<< lft.Y() << "\" z=\"" << lft.Z() << "\" /> "
<< "<left-back-bottom-point x=\"" << lbb.X() << "\" y=\""
<< lbb.Y() << "\" z=\"" << lbb.Z() << "\" /> "
<< "<right-front-bottom-point x=\"" << rfb.X() << "\" y =\""
<< rfb.Y() << "\" z=\"" << rfb.Z() << "\" /> "
<< "</cuboid>";
return xmlShapeStream.str();
}
/**
* Create the XML required to define a cylinder from the given args
* @param args A user-supplied dict of args
* @param refFrame Defines the reference frame for the shape
* @param hollow True if an annulus is to be created
* @return The XML definition string
*/
std::string
SetSample::createCylinderLikeXML(const Kernel::PropertyManager &args,
const Geometry::ReferenceFrame &refFrame,
bool hollow) const {
const std::string tag = hollow ? "hollow-cylinder" : "cylinder";
double height = args.getProperty(ShapeArgs::HEIGHT);
double innerRadius = hollow ? args.getProperty(ShapeArgs::INNER_RADIUS) : 0.0;
double outerRadius = hollow ? args.getProperty(ShapeArgs::OUTER_RADIUS)
: args.getProperty("Radius");
std::vector<double> centre = args.getProperty(ShapeArgs::CENTER);
// convert to metres
height *= 0.01;
innerRadius *= 0.01;
outerRadius *= 0.01;
std::transform(centre.begin(), centre.end(), centre.begin(),
[](double val) { return val *= 0.01; });
// XML needs center position of bottom base but user specifies center of
// cylinder
const unsigned axisIdx = static_cast<unsigned>(refFrame.pointingUp());
const V3D baseCentre = cylBaseCentre(centre, height, axisIdx);
std::ostringstream xmlShapeStream;
xmlShapeStream << "<" << tag << " id=\"sample-shape\"> "
<< "<centre-of-bottom-base x=\"" << baseCentre.X() << "\" y=\""
<< baseCentre.Y() << "\" z=\"" << baseCentre.Z() << "\" /> "
<< axisXML(axisIdx) << "<height val=\"" << height << "\" /> ";
if (hollow) {
xmlShapeStream << "<inner-radius val=\"" << innerRadius << "\"/>"
<< "<outer-radius val=\"" << outerRadius << "\"/>";
} else {
xmlShapeStream << "<radius val=\"" << outerRadius << "\"/>";
}
xmlShapeStream << "</" << tag << ">";
return xmlShapeStream.str();
}
/**
* Run SetSampleShape as an algorithm to set the shape of the sample
* @param workspace A reference to the workspace
* @param xml A string containing the XML definition
*/
void SetSample::runSetSampleShape(API::MatrixWorkspace_sptr &workspace,
const std::string &xml) {
auto alg = createChildAlgorithm("CreateSampleShape");
alg->setProperty(PropertyNames::INPUT_WORKSPACE, workspace);
alg->setProperty("ShapeXML", xml);
alg->executeAsChildAlg();
}
/**
* Run the named child algorithm on the given workspace. It assumes an in/out
* workspace property called InputWorkspace
* @param name The name of the algorithm to run
* @param workspace A reference to the workspace
* @param args A PropertyManager specifying the required arguments
*/
void SetSample::runChildAlgorithm(const std::string &name,
API::MatrixWorkspace_sptr &workspace,
const Kernel::PropertyManager &args) {
auto alg = createChildAlgorithm(name);
alg->setProperty(PropertyNames::INPUT_WORKSPACE, workspace);
alg->updatePropertyValues(args);
alg->executeAsChildAlg();
}
} // namespace DataHandling
} // namespace Mantid