IFunction.cpp

//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
#include "MantidKernel/Exception.h"
#include "MantidKernel/Logger.h"
#include "MantidAPI/IFunction.h"
#include "MantidAPI/Jacobian.h"
#include "MantidAPI/IConstraint.h"
#include "MantidAPI/ParameterTie.h"
#include "MantidAPI/Expression.h"
#include "MantidAPI/ConstraintFactory.h"
#include "MantidAPI/FunctionFactory.h"

#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/IFunctionWithLocation.h"
#include "MantidGeometry/Instrument/ParameterMap.h"
#include "MantidGeometry/Instrument/Component.h"
#include "MantidGeometry/Instrument/DetectorGroup.h"
#include "MantidGeometry/Instrument/FitParameter.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/MultiThreaded.h"
#include "MantidKernel/ProgressBase.h"
#include "MantidGeometry/muParser_Silent.h"

#include <boost/lexical_cast.hpp>

#include <Poco/StringTokenizer.h>

#include <limits>
#include <sstream>
#include <algorithm>

namespace Mantid {
namespace API {
using namespace Geometry;

namespace {
/// static logger
Kernel::Logger g_log("IFunction");
}

/**
 * Destructor
 */
IFunction::~IFunction() {
  m_attrs.clear();
  if (m_handler) {
    delete m_handler;
    m_handler = NULL;
  }
}

/**
 * Virtual copy constructor
 */
boost::shared_ptr<IFunction> IFunction::clone() const {
  return FunctionFactory::Instance().createInitialized(this->asString());
}

/**
 * Attach a progress reporter
 * @param reporter :: A pointer to a progress reporter that can be called during
 * function evaluation
 */
void IFunction::setProgressReporter(Kernel::ProgressBase *reporter) {
  m_progReporter = reporter;
  m_progReporter->setNotifyStep(0.01);
}

/**
 * If a reporter object is set, reports progress with an optional message
 * @param msg :: A message to display (default = "")
 */
void IFunction::reportProgress(const std::string &msg) const {
  if (m_progReporter) {
    const_cast<Kernel::ProgressBase *>(m_progReporter)->report(msg);
  }
}

/**
 *
 * @returns true if a progress reporter is set & evalaution has been requested
 *to stop
 */
bool IFunction::cancellationRequestReceived() const {
  if (m_progReporter)
    return m_progReporter->hasCancellationBeenRequested();
  else
    return false;
}

/** Base class implementation calculates the derivatives numerically.
 * @param domain :: The domain of the function
 * @param jacobian :: A Jacobian matrix. It is expected to have dimensions of
 * domain.size() by nParams().
 */
void IFunction::functionDeriv(const FunctionDomain &domain,
                              Jacobian &jacobian) {
  calNumericalDeriv(domain, jacobian);
}

/**
 * Ties a parameter to other parameters
 * @param parName :: The name of the parameter to tie.
 * @param expr :: A math expression
 * @param isDefault :: Flag to mark as default the value of an object associated
 * with this reference: a tie or a constraint.
 * @return newly ties parameters
 */
ParameterTie *IFunction::tie(const std::string &parName,
                             const std::string &expr, bool isDefault) {
  ParameterTie *ti = new ParameterTie(this, parName, expr, isDefault);
  addTie(ti);
  this->fix(getParameterIndex(*ti));
  return ti;
}

/**
 * Add ties to the function.
 * @param ties :: Comma-separated list of name=value pairs where name is a
 *parameter name and value
 *  is a math expression tying the parameter to other parameters or a constant.
 * @param isDefault :: Flag to mark as default the value of an object associated
 *with this reference: a tie or a constraint.
 *
 */
void IFunction::addTies(const std::string &ties, bool isDefault) {
  Expression list;
  list.parse(ties);
  list.toList();
  for (auto t = list.begin(); t != list.end(); ++t) {
    if (t->name() == "=" && t->size() >= 2) {
      size_t n = t->size() - 1;
      const std::string value = (*t)[n].str();
      for (size_t i = n; i != 0;) {
        --i;
        this->tie((*t)[i].name(), value, isDefault);
      }
    }
  }
}

/** Removes the tie off a parameter. The parameter becomes active
 * This method can be used when constructing and editing the IFunction in a GUI
 * @param parName :: The name of the parameter which ties will be removed.
 */
void IFunction::removeTie(const std::string &parName) {
  size_t i = parameterIndex(parName);
  this->removeTie(i);
}

/**
 * Writes a string that can be used in Fit.IFunction to create a copy of this
 * IFunction
 * @return string representation of the function
 */
std::string IFunction::asString() const {
  std::ostringstream ostr;
  ostr << "name=" << this->name();
  // print the attributes
  std::vector<std::string> attr = this->getAttributeNames();
  for (size_t i = 0; i < attr.size(); i++) {
    std::string attName = attr[i];
    std::string attValue = this->getAttribute(attr[i]).value();
    if (!attValue.empty() && attValue != "\"\"") {
      ostr << ',' << attName << '=' << attValue;
    }
  }
  // print the parameters
  for (size_t i = 0; i < nParams(); i++) {
    const ParameterTie *tie = getTie(i);
    if (!tie || !tie->isDefault()) {
      ostr << ',' << parameterName(i) << '=' << getParameter(i);
    }
  }
  // collect non-default constraints
  std::string constraints;
  for (size_t i = 0; i < nParams(); i++) {
    const IConstraint *c = getConstraint(i);
    if (c && !c->isDefault()) {
      std::string tmp = c->asString();
      if (!tmp.empty()) {
        if (!constraints.empty()) {
          constraints += ",";
        }
        constraints += tmp;
      }
    }
  }
  // print constraints
  if (!constraints.empty()) {
    ostr << ",constraints=(" << constraints << ")";
  }
  // collect the non-default ties
  std::string ties;
  for (size_t i = 0; i < nParams(); i++) {
    const ParameterTie *tie = getTie(i);
    if (tie && !tie->isDefault()) {
      std::string tmp = tie->asString(this);
      if (!tmp.empty()) {
        if (!ties.empty()) {
          ties += ",";
        }
        ties += tmp;
      }
    }
  }
  // print the ties
  if (!ties.empty()) {
    ostr << ",ties=(" << ties << ")";
  }
  return ostr.str();
}

/** Add a list of constraints from a string
 * @param str :: A comma-separated list of constraint expressions.
 * @param isDefault :: Flag to mark as default the value of an object associated
 *with this reference.
 *
 */
void IFunction::addConstraints(const std::string &str, bool isDefault) {
  Expression list;
  list.parse(str);
  list.toList();
  for (auto expr = list.begin(); expr != list.end(); ++expr) {
    IConstraint *c =
        ConstraintFactory::Instance().createInitialized(this, *expr, isDefault);
    this->addConstraint(c);
  }
}

/**
 * Return a vector with all parameter names.
 */
std::vector<std::string> IFunction::getParameterNames() const {
  std::vector<std::string> out;
  for (size_t i = 0; i < nParams(); ++i) {
    out.push_back(parameterName(i));
  }
  return out;
}

/** Set a function handler
 * @param handler :: A new handler
 */
void IFunction::setHandler(FunctionHandler *handler) {
  m_handler = handler;
  if (handler && handler->function().get() != this) {
    throw std::runtime_error("Function handler points to a different function");
  }
  m_handler->init();
}

/// Function to return all of the categories that contain this function
const std::vector<std::string> IFunction::categories() const {
  std::vector<std::string> res;
  Poco::StringTokenizer tokenizer(category(), categorySeparator(),
                                  Poco::StringTokenizer::TOK_TRIM |
                                      Poco::StringTokenizer::TOK_IGNORE_EMPTY);
  Poco::StringTokenizer::Iterator h = tokenizer.begin();

  for (; h != tokenizer.end(); ++h) {
    res.push_back(*h);
  }

  return res;
}

/**
 * Operator <<
 * @param ostr :: The output stream
 * @param f :: The IFunction
 */
std::ostream &operator<<(std::ostream &ostr, const IFunction &f) {
  ostr << f.asString();
  return ostr;
}

namespace {
/**
 * Const attribute visitor returning the type of the attribute
 */
class AttType : public IFunction::ConstAttributeVisitor<std::string> {
protected:
  /// Apply if string
  std::string apply(const std::string &) const { return "std::string"; }
  /// Apply if int
  std::string apply(const int &) const { return "int"; }
  /// Apply if double
  std::string apply(const double &) const { return "double"; }
  /// Apply if bool
  std::string apply(const bool &) const { return "bool"; }
  /// Apply if vector
  std::string apply(const std::vector<double> &) const {
    return "std::vector<double>";
  }
};
}

std::string IFunction::Attribute::type() const {
  AttType tmp;
  return apply(tmp);
}

namespace {
/**
 * Const attribute visitor returning the value of the attribute as a string
 */
class AttValue : public IFunction::ConstAttributeVisitor<std::string> {
public:
  AttValue(bool quoteString = false)
      : IFunction::ConstAttributeVisitor<std::string>(),
        m_quoteString(quoteString) {}

protected:
  /// Apply if string
  std::string apply(const std::string &str) const {
    return (m_quoteString) ? std::string("\"" + str + "\"") : str;
  }
  /// Apply if int
  std::string apply(const int &i) const {
    return boost::lexical_cast<std::string>(i);
  }
  /// Apply if double
  std::string apply(const double &d) const {
    return boost::lexical_cast<std::string>(d);
  }
  /// Apply if bool
  std::string apply(const bool &b) const { return b ? "true" : "false"; }
  /// Apply if vector
  std::string apply(const std::vector<double> &v) const {
    std::string res = "(";
    if (v.size() > 0) {
      for (size_t i = 0; i < v.size() - 1; ++i) {
        res += boost::lexical_cast<std::string>(v[i]) + ",";
      }
      res += boost::lexical_cast<std::string>(v.back());
    }
    res += ")";
    return res;
  }

private:
  /// Flag to quote a string value returned
  bool m_quoteString;
};
}

std::string IFunction::Attribute::value() const {
  AttValue tmp(m_quoteValue);
  return apply(tmp);
}

/**
 * Return the attribute as a string if it is a string.
 */
std::string IFunction::Attribute::asString() const {
  if (m_quoteValue)
    return asQuotedString();

  try {
    return boost::get<std::string>(m_data);
  } catch (...) {
    throw std::runtime_error("Trying to access a " + type() + " attribute "
                                                              "as string");
  }
}

/**
 * Return the attribute as a quoted string if it is a string.
 */
std::string IFunction::Attribute::asQuotedString() const {
  std::string attr;

  try {
    attr = boost::get<std::string>(m_data);
  } catch (...) {
    throw std::runtime_error("Trying to access a " + type() + " attribute "
                                                              "as string");
  }

  if (attr.empty())
    return "\"\"";

  std::string quoted(attr);
  if (*(attr.begin()) != '\"')
    quoted = "\"" + attr;
  if (*(quoted.end() - 1) != '\"')
    quoted += "\"";

  return quoted;
}

/**
 * Return the attribute as an unquoted string if it is a string.
 */
std::string IFunction::Attribute::asUnquotedString() const {
  std::string attr;

  try {
    attr = boost::get<std::string>(m_data);
  } catch (...) {
    throw std::runtime_error("Trying to access a " + type() + " attribute "
                                                              "as string");
  }
  std::string unquoted(attr);
  if (attr.empty())
    return "";
  if (*(attr.begin()) == '\"')
    unquoted = std::string(attr.begin() + 1, attr.end() - 1);
  if (*(unquoted.end() - 1) == '\"')
    unquoted = std::string(unquoted.begin(), unquoted.end() - 1);

  return unquoted;
}

/**
 * Return the attribute as an int if it is a int.
 */
int IFunction::Attribute::asInt() const {
  try {
    return boost::get<int>(m_data);
  } catch (...) {
    throw std::runtime_error("Trying to access a " + type() + " attribute "
                                                              "as int");
  }
}

/**
 * Return the attribute as a double if it is a double.
 */
double IFunction::Attribute::asDouble() const {
  try {
    return boost::get<double>(m_data);
  } catch (...) {
    throw std::runtime_error("Trying to access a " + type() + " attribute "
                                                              "as double");
  }
}

/**
 * Return the attribute as a bool if it is a bool.
 */
bool IFunction::Attribute::asBool() const {
  try {
    return boost::get<bool>(m_data);
  } catch (...) {
    throw std::runtime_error("Trying to access a " + type() + " attribute "
                                                              "as bool");
  }
}

/**
 * Return the attribute as a bool if it is a vector.
 */
std::vector<double> IFunction::Attribute::asVector() const {
  try {
    return boost::get<std::vector<double>>(m_data);
  } catch (...) {
    throw std::runtime_error("Trying to access a " + type() + " attribute "
                                                              "as vector");
  }
}

/** Sets new value if attribute is a string. If the type is wrong
 * throws an exception
 * @param str :: The new value
 */
void IFunction::Attribute::setString(const std::string &str) {
  try {
    boost::get<std::string>(m_data) = str;
  } catch (...) {
    throw std::runtime_error("Trying to access a " + type() + " attribute "
                                                              "as string");
  }
}

/** Sets new value if attribute is a double. If the type is wrong
 * throws an exception
 * @param d :: The new value
 */
void IFunction::Attribute::setDouble(const double &d) {
  try {
    boost::get<double>(m_data) = d;
  } catch (...) {
    throw std::runtime_error("Trying to access a " + type() + " attribute "
                                                              "as double");
  }
}

/** Sets new value if attribute is an int. If the type is wrong
 * throws an exception
 * @param i :: The new value
 */
void IFunction::Attribute::setInt(const int &i) {
  try {
    boost::get<int>(m_data) = i;
  } catch (...) {
    throw std::runtime_error("Trying to access a " + type() + " attribute "
                                                              "as int");
  }
}

/** Sets new value if attribute is an bool. If the type is wrong
 * throws an exception
 * @param b :: The new value
 */
void IFunction::Attribute::setBool(const bool &b) {
  try {
    boost::get<bool>(m_data) = b;
  } catch (...) {
    throw std::runtime_error("Trying to access a " + type() + " attribute "
                                                              "as bool");
  }
}

/**
 * Sets new value if attribute is a vector. If the type is wrong
 * throws an exception
 * @param v :: The new value
 */
void IFunction::Attribute::setVector(const std::vector<double> &v) {
  try {
    auto &value = boost::get<std::vector<double>>(m_data);
    value.assign(v.begin(), v.end());
  } catch (...) {
    throw std::runtime_error("Trying to access a " + type() + " attribute "
                                                              "as vector");
  }
}

namespace {
/**
 * Attribute visitor setting new value to an attribute
 */
class SetValue : public IFunction::AttributeVisitor<> {
public:
  /**
   * Constructor
   * @param value :: The value to set
   */
  SetValue(const std::string &value) : m_value(value) {}

protected:
  /// Apply if string
  void apply(std::string &str) const { str = m_value; }
  /// Apply if int
  void apply(int &i) const {
    std::istringstream istr(m_value + " ");
    istr >> i;
    if (!istr.good())
      throw std::invalid_argument("Failed to set int attribute "
                                  "from string " +
                                  m_value);
  }
  /// Apply if double
  void apply(double &d) const {
    std::istringstream istr(m_value + " ");
    istr >> d;
    if (!istr.good())
      throw std::invalid_argument("Failed to set double attribute "
                                  "from string " +
                                  m_value);
  }
  /// Apply if bool
  void apply(bool &b) const {
    b = (m_value == "true" || m_value == "TRUE" || m_value == "1");
  }
  /// Apply if vector
  void apply(std::vector<double> &v) const {
    if (m_value.empty()) {
      v.clear();
      return;
    }
    if (m_value.size() > 2) {
      // check if the value is in barckets (...)
      if (m_value[0] == '(' && m_value[m_value.size() - 1] == ')') {
        m_value.erase(0, 1);
        m_value.erase(m_value.size() - 1);
      }
    }
    Poco::StringTokenizer tokenizer(m_value, ",",
                                    Poco::StringTokenizer::TOK_TRIM);
    v.resize(tokenizer.count());
    for (size_t i = 0; i < v.size(); ++i) {
      v[i] = boost::lexical_cast<double>(tokenizer[i]);
    }
  }

private:
  mutable std::string m_value; ///<the value as a string
};
}

/** Set value from a string. Throws exception if the string has wrong format
 * @param str :: String representation of the new value
 */
void IFunction::Attribute::fromString(const std::string &str) {
  SetValue tmp(str);
  apply(tmp);
}

/// Value of i-th active parameter. Override this method to make fitted
/// parameters different from the declared
double IFunction::activeParameter(size_t i) const {
  if (!isActive(i)) {
    throw std::runtime_error("Attempt to use an inactive parameter");
  }
  return getParameter(i);
}

/// Set new value of i-th active parameter. Override this method to make fitted
/// parameters different from the declared
void IFunction::setActiveParameter(size_t i, double value) {
  if (!isActive(i)) {
    throw std::runtime_error("Attempt to use an inactive parameter");
  }
  setParameter(i, value);
}

/**
 * Returns the name of an active parameter.
 * @param i :: Index of a parameter. The parameter must be active.
 */
std::string IFunction::nameOfActive(size_t i) const {
  if (!isActive(i)) {
    throw std::runtime_error("Attempt to use an inactive parameter");
  }
  return parameterName(i);
}

/**
 * Returns the description of an active parameter.
 * @param i :: Index of a parameter. The parameter must be active.
 */
std::string IFunction::descriptionOfActive(size_t i) const {
  if (!isActive(i)) {
    throw std::runtime_error("Attempt to use an inactive parameter");
  }
  return parameterDescription(i);
}

/** Calculate numerical derivatives.
 * @param domain :: The domain of the function
 * @param jacobian :: A Jacobian matrix. It is expected to have dimensions of
 * domain.size() by nParams().
 */
void IFunction::calNumericalDeriv(const FunctionDomain &domain,
                                  Jacobian &jacobian) {
  const double minDouble = std::numeric_limits<double>::min();
  const double epsilon = std::numeric_limits<double>::epsilon() * 100;
  double stepPercentage = 0.001; // step percentage
  double step;                   // real step
  double cutoff = 100.0 * minDouble / stepPercentage;
  size_t nParam = nParams();
  size_t nData = domain.size();

  FunctionValues minusStep(domain);
  FunctionValues plusStep(domain);

  // PARALLEL_CRITICAL(numeric_deriv)
  {
    applyTies(); // just in case
    function(domain, minusStep);
  }

  for (size_t iP = 0; iP < nParam; iP++) {
    if (isActive(iP)) {
      const double val = activeParameter(iP);
      if (fabs(val) < cutoff) {
        step = epsilon;
      } else {
        step = val * stepPercentage;
      }

      double paramPstep = val + step;

      // PARALLEL_CRITICAL(numeric_deriv)
      {
        setActiveParameter(iP, paramPstep);
        applyTies();
        function(domain, plusStep);
        setActiveParameter(iP, val);
      }

      step = paramPstep - val;
      for (size_t i = 0; i < nData; i++) {
        jacobian.set(i, iP,
                     (plusStep.getCalculated(i) - minusStep.getCalculated(i)) /
                         step);
      }
    }
  }
}

/** Initialize the function providing it the workspace
 * @param workspace :: The workspace to set
 * @param wi :: The workspace index
 * @param startX :: The lower bin index
 * @param endX :: The upper bin index
 */
void IFunction::setMatrixWorkspace(
    boost::shared_ptr<const API::MatrixWorkspace> workspace, size_t wi,
    double startX, double endX) {
  UNUSED_ARG(startX);
  UNUSED_ARG(endX);

  if (!workspace)
    return; // unset the workspace

  try {

    // check if parameter are specified in instrument definition file

    const Geometry::ParameterMap &paramMap = workspace->instrumentParameters();

    Geometry::IDetector_const_sptr det;
    size_t numDetectors = workspace->getSpectrum(wi)->getDetectorIDs().size();
    if (numDetectors > 1) {
      // If several detectors are on this workspace index, just use the ID of
      // the first detector
      // Note JZ oct 2011 - I'm not sure why the code uses the first detector
      // and not the group. Ask Roman.
      Instrument_const_sptr inst = workspace->getInstrument();
      det = inst->getDetector(
          *workspace->getSpectrum(wi)->getDetectorIDs().begin());
    } else
      // Get the detector (single) at this workspace index
      det = workspace->getDetector(wi);
    ;

    for (size_t i = 0; i < nParams(); i++) {
      if (!isExplicitlySet(i)) {
        Geometry::Parameter_sptr param =
            paramMap.getRecursive(&(*det), parameterName(i), "fitting");
        if (param != Geometry::Parameter_sptr()) {
          // get FitParameter
          const Geometry::FitParameter &fitParam =
              param->value<Geometry::FitParameter>();

          // check first if this parameter is actually specified for this
          // function
          if (name().compare(fitParam.getFunction()) == 0) {
            // update value
            IFunctionWithLocation *testWithLocation =
                dynamic_cast<IFunctionWithLocation *>(this);
            if (testWithLocation == NULL ||
                (fitParam.getLookUpTable().containData() == false &&
                 fitParam.getFormula().compare("") == 0)) {
              setParameter(i, fitParam.getValue());
            } else {
              double centreValue = testWithLocation->centre();
              Kernel::Unit_sptr centreUnit; // unit of value used in formula or
                                            // to look up value in lookup table
              if (fitParam.getFormula().compare("") == 0)
                centreUnit = fitParam.getLookUpTable().getXUnit(); // from table
              else {
                if (!fitParam.getFormulaUnit().empty()) {
                  try {
                    centreUnit = Kernel::UnitFactory::Instance().create(
                        fitParam.getFormulaUnit()); // from formula
                  } catch (...) {
                    g_log.warning()
                        << fitParam.getFormulaUnit()
                        << " Is not an recognised formula unit for parameter "
                        << fitParam.getName() << "\n";
                  }
                }
              }

              // if unit specified convert centre value to unit required by
              // formula or look-up-table
              if (centreUnit) {
                g_log.debug()
                    << "For FitParameter " << parameterName(i)
                    << " centre of peak before any unit convertion is "
                    << centreValue << std::endl;
                centreValue =
                    convertValue(centreValue, centreUnit, workspace, wi);
                g_log.debug() << "For FitParameter " << parameterName(i)
                              << " centre of peak after any unit convertion is "
                              << centreValue << std::endl;
              }

              double paramValue = fitParam.getValue(centreValue);

              // this returned param value by a formula or a look-up-table may
              // have
              // a unit of its own. If set convert param value
              // See section 'Using fitting parameters in
              // www.mantidproject.org/IDF
              if (fitParam.getFormula().compare("") == 0) {
                // so from look up table
                Kernel::Unit_sptr resultUnit =
                    fitParam.getLookUpTable().getYUnit(); // from table
                g_log.debug() << "The FitParameter " << parameterName(i)
                              << " = " << paramValue
                              << " before y-unit convertion" << std::endl;
                paramValue /= convertValue(1.0, resultUnit, workspace, wi);
                g_log.debug() << "The FitParameter " << parameterName(i)
                              << " = " << paramValue
                              << " after y-unit convertion" << std::endl;
              } else {
                // so from formula

                std::string resultUnitStr = fitParam.getResultUnit();

                if (!resultUnitStr.empty()) {
                  std::vector<std::string> allUnitStr =
                      Kernel::UnitFactory::Instance().getKeys();
                  for (unsigned iUnit = 0; iUnit < allUnitStr.size(); iUnit++) {
                    size_t found = resultUnitStr.find(allUnitStr[iUnit]);
                    if (found != std::string::npos) {
                      size_t len = allUnitStr[iUnit].size();
                      std::stringstream readDouble;
                      Kernel::Unit_sptr unt =
                          Kernel::UnitFactory::Instance().create(
                              allUnitStr[iUnit]);
                      readDouble << 1.0 / convertValue(1.0, unt, workspace, wi);
                      resultUnitStr.replace(found, len, readDouble.str());
                    }
                  } // end for

                  try {
                    mu::Parser p;
                    p.SetExpr(resultUnitStr);
                    g_log.debug() << "The FitParameter " << parameterName(i)
                                  << " = " << paramValue
                                  << " before result-unit convertion (using "
                                  << resultUnitStr << ")" << std::endl;
                    paramValue *= p.Eval();
                    g_log.debug() << "The FitParameter " << parameterName(i)
                                  << " = " << paramValue
                                  << " after result-unit convertion"
                                  << std::endl;
                  } catch (mu::Parser::exception_type &e) {
                    g_log.error()
                        << "Cannot convert formula unit to workspace unit"
                        << " Formula unit which cannot be passed is "
                        << resultUnitStr
                        << ". Muparser error message is: " << e.GetMsg()
                        << std::endl;
                  }
                } // end if
              } // end trying to convert result-unit from formula or y-unit for
              // lookuptable

              setParameter(i, paramValue);
            } // end of update parameter value

            // add tie if specified for this parameter in instrument definition
            // file
            if (fitParam.getTie().compare("")) {
              std::ostringstream str;
              str << getParameter(i);
              tie(parameterName(i), str.str());
            }

            // add constraint if specified for this parameter in instrument
            // definition file
            if (fitParam.getConstraint().compare("")) {
              IConstraint *constraint =
                  ConstraintFactory::Instance().createInitialized(
                      this, fitParam.getConstraint());
              if (fitParam.getConstraintPenaltyFactor().compare("")) {
                try {
                  double penalty =
                      atof(fitParam.getConstraintPenaltyFactor().c_str());
                  constraint->setPenaltyFactor(penalty);
                } catch (...) {
                  g_log.warning()
                      << "Can't set penalty factor for constraint\n";
                }
              }
              addConstraint(constraint);
            }
          }
        }
      }
    }
  } catch (...) {
  }
}

/** Convert a value from unit defined in workspace (ws) to outUnit
 *
 *  @param value ::   assumed to be in unit of workspace
 *  @param outUnit ::  unit to convert to
 *  @param ws ::      workspace
 *  @param wsIndex :: workspace index
 *  @return converted value
 */
double IFunction::convertValue(double value, Kernel::Unit_sptr &outUnit,
                               boost::shared_ptr<const MatrixWorkspace> ws,
                               size_t wsIndex) const {
  // only required if formula or look-up-table different from ws unit
  const auto &wsUnit = ws->getAxis(0)->unit();
  if (outUnit->unitID().compare(wsUnit->unitID()) == 0)
    return value;

  // first check if it is possible to do a quick conversion and convert
  // slight duplication to below to avoid instantiating vector unless necessary
  double factor(0.0), power(0.0);
  if (wsUnit->quickConversion(*outUnit, factor, power)) {
    return factor * std::pow(value, power);
  } else {
    std::vector<double> singleValue(1, value);
    convertValue(singleValue, outUnit, ws, wsIndex);
    return singleValue.front();
  }
}

/** Convert values from unit defined in workspace (ws) to outUnit
 *
 *  @param values ::   As input: assumed to be in unit of workspace.
 *                  As output: in unit of outUnit
 *  @param outUnit ::  unit to convert to
 *  @param ws ::      workspace
 *  @param wsIndex :: workspace index
 */
void IFunction::convertValue(std::vector<double> &values,
                             Kernel::Unit_sptr &outUnit,
                             boost::shared_ptr<const MatrixWorkspace> ws,
                             size_t wsIndex) const {
  // only required if  formula or look-up-table different from ws unit
  const auto &wsUnit = ws->getAxis(0)->unit();
  if (outUnit->unitID().compare(wsUnit->unitID()) == 0)
    return;

  // first check if it is possible to do a quick conversion convert
  double factor, power;
  if (wsUnit->quickConversion(*outUnit, factor, power)) {
    auto iend = values.end();
    for (auto itr = values.begin(); itr != iend; ++itr)
      (*itr) = factor * std::pow(*itr, power);
  } else {
    // Get l1, l2 and theta  (see also RemoveBins.calculateDetectorPosition())
    Instrument_const_sptr instrument = ws->getInstrument();
    Geometry::IComponent_const_sptr sample = instrument->getSample();
    if (sample == NULL) {
      g_log.error()
          << "No sample defined instrument. Cannot convert units for function\n"
          << "Ignore convertion.";
      return;
    }
    double l1 = instrument->getSource()->getDistance(*sample);
    Geometry::IDetector_const_sptr det = ws->getDetector(wsIndex);
    double l2(-1.0), twoTheta(0.0);
    if (!det->isMonitor()) {
      l2 = det->getDistance(*sample);
      twoTheta = ws->detectorTwoTheta(det);
    } else // If this is a monitor then make l1+l2 = source-detector distance
           // and twoTheta=0
    {
      l2 = det->getDistance(*(instrument->getSource()));
      l2 = l2 - l1;
      twoTheta = 0.0;
    }
    int emode = static_cast<int>(ws->getEMode());
    double efixed(0.0);
    try {
      efixed = ws->getEFixed(det);
    } catch (std::exception &) {
      // assume elastic
      efixed = 0.0;
      emode = 0;
    }

    std::vector<double> emptyVec;
    wsUnit->toTOF(values, emptyVec, l1, l2, twoTheta, emode, efixed, 0.0);
    outUnit->fromTOF(values, emptyVec, l1, l2, twoTheta, emode, efixed, 0.0);
  }
}

/**
* Returns the number of attributes associated with the function
*/
size_t IFunction::nAttributes() const { return m_attrs.size(); }

/// Check if attribute named exists
bool IFunction::hasAttribute(const std::string &name) const {
  return m_attrs.find(name) != m_attrs.end();
}

/**
  * Overload for const char* values.
  * @param attName :: Attribute name
  * @param value :: New attribute value to set
  */
void IFunction::setAttributeValue(const std::string &attName,
                                  const char *value) {
  std::string str(value);
  setAttributeValue(attName, str);
}

/**
  * Set string attribute by value. Make sure that quoted style doesn't change.
  * @param attName :: Attribute name
  * @param value :: New attribute value to set
  */
void IFunction::setAttributeValue(const std::string &attName,
                                  const std::string &value) {
  Attribute att = getAttribute(attName);
  att.setString(value);
  setAttribute(attName, att);
}

/// Returns a list of attribute names
std::vector<std::string> IFunction::getAttributeNames() const {
  std::vector<std::string> names(nAttributes(), "");
  size_t index(0);
  for (auto iter = m_attrs.begin(); iter != m_attrs.end(); ++iter) {
    names[index] = iter->first;
    ++index;
  }
  return names;
}

/**
* Return a value of attribute attName
* @param name :: Returns the named attribute
*/
API::IFunction::Attribute
IFunction::getAttribute(const std::string &name) const {
  if (hasAttribute(name)) {
    return m_attrs.at(name);
  } else {
    throw std::invalid_argument(
        "ParamFunctionAttributeHolder::getAttribute - Unknown attribute '" +
        name + "'");
  }
}

/**
*  Set a value to a named attribute. Can be overridden in the inheriting class,
* the default
*  just stores the value
*  @param name :: The name of the attribute
*  @param value :: The value of the attribute
*/
void IFunction::setAttribute(const std::string &name,
                             const API::IFunction::Attribute &value) {
  storeAttributeValue(name, value);
}

/**
* Declares a single attribute
* @param name :: The name of the attribute
* @param defaultValue :: A default value
*/
void IFunction::declareAttribute(
    const std::string &name, const API::IFunction::Attribute &defaultValue) {
  m_attrs.insert(std::make_pair(name, defaultValue));
}

/// Initialize the function. Calls declareAttributes & declareParameters
void IFunction::init() {
  declareAttributes();
  declareParameters();
}

/**
*  Set a value to a named attribute
*  @param name :: The name of the attribute
*  @param value :: The value of the attribute
*/
void IFunction::storeAttributeValue(const std::string &name,
                                    const API::IFunction::Attribute &value) {
  if (hasAttribute(name)) {
    m_attrs[name] = value;
  } else {
    throw std::invalid_argument(
        "ParamFunctionAttributeHolder::setAttribute - Unknown attribute '" +
        name + "'");
  }
}

/**
 * Set the covariance matrix. Algorithm Fit sets this matrix to the top-level
 * function
 * after fitting. If the function is composite the matrix isn't set to its
 * members.
 * The matrix must be square and its size equal to the number of parameters of
 * this function.
 * @param covar :: A matrix to set.
 */
void IFunction::setCovarianceMatrix(
    boost::shared_ptr<Kernel::Matrix<double>> covar) {
  // the matrix shouldn't be empty
  if (!covar) {
    throw std::invalid_argument(
        "IFunction: Cannot set an empty covariance matrix");
  }
  // the matrix should relate to this function
  if (covar->numRows() != nParams() || covar->numCols() != nParams()) {
    throw std::invalid_argument(
        "IFunction: Covariance matrix has a wrong size");
  }
  m_covar = covar;
}

} // namespace API
} // namespace Mantid

///\cond TEMPLATE
namespace Mantid {
namespace Kernel {

template <>
MANTID_API_DLL boost::shared_ptr<Mantid::API::IFunction>
IPropertyManager::getValue<boost::shared_ptr<Mantid::API::IFunction>>(
    const std::string &name) const {
  PropertyWithValue<boost::shared_ptr<Mantid::API::IFunction>> *prop =
      dynamic_cast<
          PropertyWithValue<boost::shared_ptr<Mantid::API::IFunction>> *>(
          getPointerToProperty(name));
  if (prop) {
    return *prop;
  } else {
    std::string message = "Attempt to assign property " + name +
                          " to incorrect type. Expected IFitFunction.";
    throw std::runtime_error(message);
  }
}

} // namespace Kernel
} // namespace Mantid
///\endcond TEMPLATE