#include "MantidHistogramData/LinearGenerator.h"
#include "MantidAlgorithms/CreateSampleWorkspace.h"
#include "MantidAPI/Axis.h"
#include "MantidAPI/FunctionFactory.h"
#include "MantidAPI/FunctionDomain1D.h"
#include "MantidAPI/FunctionProperty.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/WorkspaceCreation.h"
#include "MantidGeometry/Objects/ShapeFactory.h"
#include "MantidGeometry/Instrument/ReferenceFrame.h"
#include "MantidGeometry/Instrument/RectangularDetector.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/MersenneTwister.h"
#include "MantidIndexing/IndexInfo.h"
#include "MantidIndexing/MakeRange.h"
#include <cmath>
#include <ctime>
#include <numeric>
#include <stdexcept>
namespace Mantid {
namespace Algorithms {
using namespace Kernel;
using namespace API;
using namespace Geometry;
using namespace DataObjects;
using namespace HistogramData;
using namespace Indexing;
using Mantid::MantidVec;
using Mantid::MantidVecPtr;
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(CreateSampleWorkspace)
//----------------------------------------------------------------------------------------------
/** Constructor
*/
CreateSampleWorkspace::CreateSampleWorkspace() : m_randGen(nullptr) {}
//----------------------------------------------------------------------------------------------
/** Destructor
*/
CreateSampleWorkspace::~CreateSampleWorkspace() { delete m_randGen; }
//----------------------------------------------------------------------------------------------
/// Algorithm's name for identification. @see Algorithm::name
const std::string CreateSampleWorkspace::name() const {
return "CreateSampleWorkspace";
}
/// Algorithm's version for identification. @see Algorithm::version
int CreateSampleWorkspace::version() const { return 1; }
/// Algorithm's category for identification. @see Algorithm::category
const std::string CreateSampleWorkspace::category() const {
return "Utility\\Workspaces";
}
//----------------------------------------------------------------------------------------------
/** Initialize the algorithm's properties.
*/
void CreateSampleWorkspace::init() {
declareProperty(make_unique<WorkspaceProperty<>>("OutputWorkspace", "",
Direction::Output),
"An output workspace.");
std::vector<std::string> typeOptions{"Histogram", "Event"};
declareProperty("WorkspaceType", "Histogram",
boost::make_shared<StringListValidator>(typeOptions),
"The type of workspace to create (default: Histogram)");
// pre-defined function strings these use $PCx$ to define peak centres values
// that will be replaced before use
//$PC0$ is the far left of the data, and $PC10$ is the far right, and
// therefore will often not be used
//$PC5$ is the centre of the data
m_preDefinedFunctionmap.emplace(
"One Peak", "name=LinearBackground, A0=0.3; name=Gaussian, "
"PeakCentre=$PC5$, Height=10, Sigma=0.7;");
m_preDefinedFunctionmap.emplace(
"Multiple Peaks", "name=LinearBackground, A0=0.3;name=Gaussian, "
"PeakCentre=$PC3$, Height=10, Sigma=0.7;name=Gaussian, "
"PeakCentre=$PC6$, Height=8, Sigma=0.5");
m_preDefinedFunctionmap.emplace("Flat background",
"name=LinearBackground, A0=1;");
m_preDefinedFunctionmap.emplace("Exp Decay",
"name=ExpDecay, Height=100, Lifetime=1000;");
m_preDefinedFunctionmap.emplace(
"Powder Diffraction",
"name= LinearBackground,A0=0.0850208,A1=-4.89583e-06;"
"name=Gaussian,Height=0.584528,PeakCentre=$PC1$,Sigma=14.3772;"
"name=Gaussian,Height=1.33361,PeakCentre=$PC2$,Sigma=15.2516;"
"name=Gaussian,Height=1.74691,PeakCentre=$PC3$,Sigma=15.8395;"
"name=Gaussian,Height=0.950388,PeakCentre=$PC4$,Sigma=19.8408;"
"name=Gaussian,Height=1.92185,PeakCentre=$PC5$,Sigma=18.0844;"
"name=Gaussian,Height=3.64069,PeakCentre=$PC6$,Sigma=19.2404;"
"name=Gaussian,Height=2.8998,PeakCentre=$PC7$,Sigma=21.1127;"
"name=Gaussian,Height=2.05237,PeakCentre=$PC8$,Sigma=21.9932;"
"name=Gaussian,Height=8.40976,PeakCentre=$PC9$,Sigma=25.2751;");
m_preDefinedFunctionmap.emplace(
"Quasielastic", "name=Lorentzian,FWHM=0.3,PeakCentre=$PC5$,Amplitude=0.8;"
"name=Lorentzian,FWHM=0.1,PeakCentre=$PC5$,Amplitude=1;"
"name=LinearBackground,A0=0.1");
m_preDefinedFunctionmap.emplace(
"Quasielastic Tunnelling",
"name=LinearBackground,A0=0.1;"
"name=Lorentzian,FWHM=0.1,PeakCentre=$PC5$,Amplitude=1;"
"name=Lorentzian,FWHM=0.05,PeakCentre=$PC7$,Amplitude=0.04;"
"name=Lorentzian,FWHM=0.05,PeakCentre=$PC3$,Amplitude=0.04;"
"name=Lorentzian,FWHM=0.05,PeakCentre=$PC8$,Amplitude=0.02;"
"name=Lorentzian,FWHM=0.05,PeakCentre=$PC2$,Amplitude=0.02");
m_preDefinedFunctionmap.emplace("User Defined", "");
std::vector<std::string> functionOptions;
functionOptions.reserve(m_preDefinedFunctionmap.size());
for (const auto &preDefinedFunction : m_preDefinedFunctionmap) {
functionOptions.push_back(preDefinedFunction.first);
}
declareProperty("Function", "One Peak",
boost::make_shared<StringListValidator>(functionOptions),
"Preset options of the data to fill the workspace with");
declareProperty(
"UserDefinedFunction", "",
"Parameters defining the fitting function and its initial values");
declareProperty("NumBanks", 2,
boost::make_shared<BoundedValidator<int>>(0, 100),
"The Number of banks in the instrument (default:2)");
declareProperty("BankPixelWidth", 10,
boost::make_shared<BoundedValidator<int>>(0, 10000),
"The number of pixels in horizontally and vertically in a "
"bank (default:10)");
declareProperty("NumEvents", 1000,
boost::make_shared<BoundedValidator<int>>(0, 100000),
"The number of events per detector, this is only used for "
"EventWorkspaces (default:1000)");
declareProperty(
"Random", false,
"Whether to randomise the placement of events and data (default:false)");
declareProperty("XUnit", "TOF",
"The unit to assign to the XAxis (default:\"TOF\")");
declareProperty("XMin", 0.0, "The minimum X axis value (default:0)");
declareProperty("XMax", 20000.0, "The maximum X axis value (default:20000)");
declareProperty("BinWidth", 200.0,
boost::make_shared<BoundedValidator<double>>(0, 100000, true),
"The bin width of the X axis (default:200)");
declareProperty("PixelSpacing", 0.008,
boost::make_shared<BoundedValidator<double>>(0, 100000, true),
"The spacing between detector pixels in M (default:0.008)");
declareProperty("BankDistanceFromSample", 5.0,
boost::make_shared<BoundedValidator<double>>(0, 1000, true),
"The distance along the beam direction from the sample to "
"bank in M (default:5.0)");
declareProperty("SourceDistanceFromSample", 10.0,
boost::make_shared<BoundedValidator<double>>(0, 1000, true),
"The distance along the beam direction from the source to "
"the sample in M (default:10.0)");
}
//----------------------------------------------------------------------------------------------
/** Execute the algorithm.
*/
void CreateSampleWorkspace::exec() {
const std::string wsType = getProperty("WorkspaceType");
const std::string preDefinedFunction = getProperty("Function");
const std::string userDefinedFunction = getProperty("UserDefinedFunction");
const int numBanks = getProperty("NumBanks");
const int bankPixelWidth = getProperty("BankPixelWidth");
const int numEvents = getProperty("NumEvents");
const bool isRandom = getProperty("Random");
const std::string xUnit = getProperty("XUnit");
const double xMin = getProperty("XMin");
const double xMax = getProperty("XMax");
double binWidth = getProperty("BinWidth");
const double pixelSpacing = getProperty("PixelSpacing");
const double bankDistanceFromSample = getProperty("BankDistanceFromSample");
const double sourceSampleDistance = getProperty("SourceDistanceFromSample");
if (xMax <= xMin) {
throw std::invalid_argument("XMax must be larger than XMin");
}
if (binWidth > (xMax - xMin)) {
// the bin width is so large that there is less than one bin - so adjust it
// down
binWidth = xMax - xMin;
g_log.warning() << "The bin width is so large that there is less than one "
"bin - it has been changed to " << binWidth << '\n';
}
std::string functionString;
if (m_preDefinedFunctionmap.find(preDefinedFunction) !=
m_preDefinedFunctionmap.end()) {
// extract pre-defined string
functionString = m_preDefinedFunctionmap[preDefinedFunction];
}
if (functionString.empty()) {
functionString = userDefinedFunction;
}
if (!m_randGen) {
int seedValue = 0;
if (isRandom) {
seedValue = static_cast<int>(std::time(nullptr));
}
m_randGen = new Kernel::MersenneTwister(seedValue);
}
int numPixels = numBanks * bankPixelWidth * bankPixelWidth;
Progress progress(this, 0, 1, numBanks);
// Create an instrument with one or more rectangular banks.
Instrument_sptr inst = createTestInstrumentRectangular(
progress, numBanks, bankPixelWidth, pixelSpacing, bankDistanceFromSample,
sourceSampleDistance);
int num_bins = static_cast<int>((xMax - xMin) / binWidth);
MatrixWorkspace_sptr ws;
if (wsType == "Event") {
ws = createEventWorkspace(numPixels, num_bins, numEvents, xMin, binWidth,
bankPixelWidth * bankPixelWidth, inst,
functionString, isRandom);
} else {
ws = createHistogramWorkspace(numPixels, num_bins, xMin, binWidth,
bankPixelWidth * bankPixelWidth, inst,
functionString, isRandom);
}
// add chopper
this->addChopperParameters(ws);
// Set the Unit of the X Axis
try {
ws->getAxis(0)->unit() = UnitFactory::Instance().create(xUnit);
} catch (Exception::NotFoundError &) {
ws->getAxis(0)->unit() = UnitFactory::Instance().create("Label");
Unit_sptr unit = ws->getAxis(0)->unit();
boost::shared_ptr<Units::Label> label =
boost::dynamic_pointer_cast<Units::Label>(unit);
label->setLabel(xUnit, xUnit);
}
ws->setYUnit("Counts");
ws->setTitle("Test Workspace");
DateAndTime run_start("2010-01-01T00:00:00");
DateAndTime run_end("2010-01-01T01:00:00");
Run &theRun = ws->mutableRun();
// belt and braces use both approaches for setting start and end times
theRun.setStartAndEndTime(run_start, run_end);
theRun.addLogData(new PropertyWithValue<std::string>(
"run_start", run_start.toISO8601String()));
theRun.addLogData(
new PropertyWithValue<std::string>("run_end", run_end.toISO8601String()));
// Assign it to the output workspace property
setProperty("OutputWorkspace", ws);
;
}
/** Add chopper to the existing matrix workspace
@param ws -- shared pointer to existing matrix workspace which has instrument
and chopper
@returns workspace modified to have Fermi chopper added to it.
*/
void CreateSampleWorkspace::addChopperParameters(
API::MatrixWorkspace_sptr &ws) {
auto testInst = ws->getInstrument();
auto chopper = testInst->getComponentByName("chopper-position");
// add chopper parameters
auto ¶mMap = ws->instrumentParameters();
const std::string description(
"The initial rotation phase of the disk used to calculate the time"
" for neutrons arriving at the chopper according to the formula time = "
"delay + initial_phase/Speed");
paramMap.add<double>("double", chopper.get(), "initial_phase", -3000.,
&description);
paramMap.add<std::string>("string", chopper.get(), "ChopperDelayLog",
"fermi_delay");
paramMap.add<std::string>("string", chopper.get(), "ChopperSpeedLog",
"fermi_speed");
paramMap.add<std::string>("string", chopper.get(), "FilterBaseLog",
"is_running");
paramMap.add<bool>("bool", chopper.get(), "filter_with_derivative", false);
}
/** Create histogram workspace
*/
MatrixWorkspace_sptr CreateSampleWorkspace::createHistogramWorkspace(
int numPixels, int numBins, double x0, double binDelta,
int start_at_pixelID, Geometry::Instrument_sptr inst,
const std::string &functionString, bool isRandom) {
BinEdges x(numBins + 1, LinearGenerator(x0, binDelta));
std::vector<double> xValues(cbegin(x), cend(x) - 1);
Counts y(evalFunction(functionString, xValues, isRandom ? 1 : 0));
CountStandardDeviations e(CountVariances(y.cbegin(), y.cend()));
Indexing::IndexInfo indexInfo(numPixels);
indexInfo.setDetectorIDs(
makeRange(start_at_pixelID, start_at_pixelID + numPixels - 1));
auto retVal = create<Workspace2D>(indexInfo, Histogram(x, y, e));
retVal->setInstrument(inst);
return retVal;
}
/** Create event workspace
*/
EventWorkspace_sptr CreateSampleWorkspace::createEventWorkspace(
int numPixels, int numBins, int numEvents, double x0, double binDelta,
int start_at_pixelID, Geometry::Instrument_sptr inst,
const std::string &functionString, bool isRandom) {
DateAndTime run_start("2010-01-01T00:00:00");
Indexing::IndexInfo indexInfo(numPixels);
indexInfo.setDetectorIDs(
makeRange(start_at_pixelID, start_at_pixelID + numPixels - 1));
// add one to the number of bins as this is histogram
int numXBins = numBins + 1;
BinEdges x(numXBins, LinearGenerator(x0, binDelta));
auto retVal = create<EventWorkspace>(indexInfo, Histogram(x));
retVal->setInstrument(inst);
std::vector<double> xValues(x.cbegin(), x.cend() - 1);
std::vector<double> yValues =
evalFunction(functionString, xValues, isRandom ? 1 : 0);
// we need to normalise the results and then multiply by the number of events
// to find the events per bin
double sum_of_elems = std::accumulate(yValues.begin(), yValues.end(), 0.0);
double event_distrib_factor = numEvents / sum_of_elems;
std::transform(yValues.begin(), yValues.end(), yValues.begin(),
std::bind1st(std::multiplies<double>(), event_distrib_factor));
// the array should now contain the number of events required per bin
// Make fake events
size_t workspaceIndex = 0;
const double hourInSeconds = 60 * 60;
for (int wi = 0; wi < numPixels; wi++) {
EventList &el = retVal->getSpectrum(workspaceIndex);
for (int i = 0; i < numBins; ++i) {
// create randomised events within the bin to match the number required -
// calculated in yValues earlier
int eventsInBin = static_cast<int>(yValues[i]);
for (int q = 0; q < eventsInBin; q++) {
DateAndTime pulseTime =
run_start + (m_randGen->nextValue() * hourInSeconds);
el += TofEvent((i + m_randGen->nextValue()) * binDelta, pulseTime);
}
}
workspaceIndex++;
}
return retVal;
}
//----------------------------------------------------------------------------------------------
/**
* Evaluates a function and returns the values as a vector
*
*
* @param functionString :: the function string
* @param xVal :: A vector of the x values
* @param noiseScale :: A scaling factor for niose to be added to the data, 0=
*no noise
* @returns the calculated values
*/
std::vector<double>
CreateSampleWorkspace::evalFunction(const std::string &functionString,
const std::vector<double> &xVal,
double noiseScale = 0) {
size_t xSize = xVal.size();
// replace $PCx$ values
std::string parsedFuncString = functionString;
for (int x = 0; x <= 10; ++x) {
// get the rough peak centre value
int index = static_cast<int>((xSize / 10) * x);
if ((x == 10) && (index > 0))
--index;
double replace_val = xVal[index];
std::ostringstream tokenStream;
tokenStream << "$PC" << x << "$";
std::string token = tokenStream.str();
std::string replaceStr = boost::lexical_cast<std::string>(replace_val);
replaceAll(parsedFuncString, token, replaceStr);
}
IFunction_sptr func_sptr =
FunctionFactory::Instance().createInitialized(parsedFuncString);
FunctionDomain1DVector fd(xVal);
FunctionValues fv(fd);
func_sptr->function(fd, fv);
std::vector<double> results;
results.resize(xSize);
for (size_t x = 0; x < xSize; ++x) {
results[x] = fv.getCalculated(x);
if (noiseScale != 0) {
results[x] += ((m_randGen->nextValue() - 0.5) * noiseScale);
}
// no negative values please - it messes up the error calculation
results[x] = fabs(results[x]);
}
return results;
}
void CreateSampleWorkspace::replaceAll(std::string &str,
const std::string &from,
const std::string &to) {
if (from.empty())
return;
size_t start_pos = 0;
while ((start_pos = str.find(from, start_pos)) != std::string::npos) {
str.replace(start_pos, from.length(), to);
start_pos += to.length(); // In case 'to' contains 'from', like replacing
// 'x' with 'yx'
}
}
//----------------------------------------------------------------------------------------------
/**
* Create an test instrument with n panels of rectangular detectors,
*pixels*pixels in size,
* a source and spherical sample shape.
*
* Banks' lower-left corner is at position (0,0,5*banknum) and they go up to
*(pixels*0.008, pixels*0.008, Z)
* Pixels are 4 mm wide.
*
* @param progress :: progress indicator
* @param num_banks :: number of rectangular banks to create
* @param pixels :: number of pixels in each direction.
* @param pixelSpacing :: padding between pixels
* @param bankDistanceFromSample :: Distance of first bank from sample (defaults
*to 5.0m)
* @param sourceSampleDistance :: The distance from the source to the sample
* @returns A shared pointer to the generated instrument
*/
Instrument_sptr CreateSampleWorkspace::createTestInstrumentRectangular(
API::Progress &progress, int num_banks, int pixels, double pixelSpacing,
const double bankDistanceFromSample, const double sourceSampleDistance) {
auto testInst = boost::make_shared<Instrument>("basic_rect");
// The instrument is going to be set up with z as the beam axis and y as the
// vertical axis.
testInst->setReferenceFrame(
boost::make_shared<ReferenceFrame>(Y, Z, Left, ""));
const double cylRadius(pixelSpacing / 2);
const double cylHeight(0.0002);
// One object
Object_sptr pixelShape = createCappedCylinder(
cylRadius, cylHeight, V3D(0.0, -cylHeight / 2.0, 0.0), V3D(0., 1.0, 0.),
"pixel-shape");
for (int banknum = 1; banknum <= num_banks; banknum++) {
// Make a new bank
std::ostringstream bankname;
bankname << "bank" << banknum;
RectangularDetector *bank = new RectangularDetector(bankname.str());
bank->initialize(pixelShape, pixels, 0.0, pixelSpacing, pixels, 0.0,
pixelSpacing, banknum * pixels * pixels, true, pixels);
// Mark them all as detectors
for (int x = 0; x < pixels; x++)
for (int y = 0; y < pixels; y++) {
boost::shared_ptr<Detector> detector = bank->getAtXY(x, y);
if (detector)
// Mark it as a detector (add to the instrument cache)
testInst->markAsDetector(detector.get());
}
testInst->add(bank);
// Set the bank along the z-axis of the instrument. (beam direction).
bank->setPos(V3D(0.0, 0.0, bankDistanceFromSample * banknum));
progress.report();
}
// Define a source component
ObjComponent *source =
new ObjComponent("moderator", Object_sptr(new Object), testInst.get());
source->setPos(V3D(0.0, 0.0, -sourceSampleDistance));
testInst->add(source);
testInst->markAsSource(source);
// Add chopper
ObjComponent *chopper = new ObjComponent(
"chopper-position", Object_sptr(new Object), testInst.get());
chopper->setPos(V3D(0.0, 0.0, -0.25 * sourceSampleDistance));
testInst->add(chopper);
// Define a sample as a simple sphere
Object_sptr sampleSphere =
createSphere(0.001, V3D(0.0, 0.0, 0.0), "sample-shape");
ObjComponent *sample =
new ObjComponent("sample", sampleSphere, testInst.get());
testInst->setPos(0.0, 0.0, 0.0);
testInst->add(sample);
testInst->markAsSamplePos(sample);
return testInst;
}
//----------------------------------------------------------------------------------------------
/**
* Create a capped cylinder object
*/
Object_sptr CreateSampleWorkspace::createCappedCylinder(double radius,
double height,
const V3D &baseCentre,
const V3D &axis,
const std::string &id) {
std::ostringstream xml;
xml << "<cylinder id=\"" << id << "\">"
<< "<centre-of-bottom-base x=\"" << baseCentre.X() << "\" y=\""
<< baseCentre.Y() << "\" z=\"" << baseCentre.Z() << "\"/>"
<< "<axis x=\"" << axis.X() << "\" y=\"" << axis.Y() << "\" z=\""
<< axis.Z() << "\"/>"
<< "<radius val=\"" << radius << "\" />"
<< "<height val=\"" << height << "\" />"
<< "</cylinder>";
ShapeFactory shapeMaker;
return shapeMaker.createShape(xml.str());
}
//----------------------------------------------------------------------------------------------
/**
* Create a sphere object
*/
Object_sptr CreateSampleWorkspace::createSphere(double radius,
const V3D ¢re,
const std::string &id) {
ShapeFactory shapeMaker;
std::ostringstream xml;
xml << "<sphere id=\"" << id << "\">"
<< "<centre x=\"" << centre.X() << "\" y=\"" << centre.Y() << "\" z=\""
<< centre.Z() << "\" />"
<< "<radius val=\"" << radius << "\" />"
<< "</sphere>";
return shapeMaker.createShape(xml.str());
}
} // namespace Algorithms
} // namespace Mantid