/**
 * Calls Gaussian1D as a child algorithm to fit the offset peak in a spectrum
 * @param mosaic
 * @param rcrystallite
 * @param inname
 * @param corrOption
 * @param pointOption
 * @param tofParams
 * @return
 */
double OptimizeExtinctionParameters::fitMosaic(
    double mosaic, double rcrystallite, std::string inname,
    std::string corrOption, std::string pointOption, std::string tofParams) {
  PeaksWorkspace_sptr inputW = boost::dynamic_pointer_cast<PeaksWorkspace>(
      AnalysisDataService::Instance().retrieve(inname));
  std::vector<double> tofParam =
      Kernel::VectorHelper::splitStringIntoVector<double>(tofParams);
  if (mosaic < 0.0 || rcrystallite < 0.0)
    return 1e300;

  API::IAlgorithm_sptr tofextinction =
      createChildAlgorithm("TOFExtinction", 0.0, 0.2);
  tofextinction->setProperty("InputWorkspace", inputW);
  tofextinction->setProperty("OutputWorkspace", "tmp");
  tofextinction->setProperty("ExtinctionCorrectionType", corrOption);
  tofextinction->setProperty<double>("Mosaic", mosaic);
  tofextinction->setProperty<double>("Cell", tofParam[0]);
  tofextinction->setProperty<double>("RCrystallite", rcrystallite);
  tofextinction->executeAsChildAlg();
  PeaksWorkspace_sptr peaksW = tofextinction->getProperty("OutputWorkspace");

  API::IAlgorithm_sptr sorthkl = createChildAlgorithm("SortHKL", 0.0, 0.2);
  sorthkl->setProperty("InputWorkspace", peaksW);
  sorthkl->setProperty("OutputWorkspace", peaksW);
  sorthkl->setProperty("PointGroup", pointOption);
  sorthkl->executeAsChildAlg();
  double Chisq = sorthkl->getProperty("OutputChi2");
  std::cout << mosaic << "  " << rcrystallite << "  " << Chisq << "\n";
  return Chisq;
}

/**
 * Places the detector at the right sample_detector_distance
 */
void LoadSpice2D::moveDetector(double sample_detector_distance,
                               double translation_distance) {
  // Some tests fail if the detector is moved here.
  // TODO: Move the detector here and not the SANSLoad
  UNUSED_ARG(translation_distance);

  // Move the detector to the right position
  API::IAlgorithm_sptr mover = createChildAlgorithm("MoveInstrumentComponent");

  // Finding the name of the detector object.
  std::string detID =
      m_workspace->getInstrument()->getStringParameter("detector-name")[0];

  g_log.information("Moving " + detID);
  try {
    mover->setProperty<API::MatrixWorkspace_sptr>("Workspace", m_workspace);
    mover->setProperty("ComponentName", detID);
    mover->setProperty("Z", sample_detector_distance / 1000.0);
    // mover->setProperty("X", -translation_distance);
    mover->execute();
  } catch (std::invalid_argument &e) {
    g_log.error("Invalid argument to MoveInstrumentComponent Child Algorithm");
    g_log.error(e.what());
  } catch (std::runtime_error &e) {
    g_log.error(
        "Unable to successfully run MoveInstrumentComponent Child Algorithm");
    g_log.error(e.what());
  }
}

/** Handler of the start notifications. Adds an algorithm call to the script.
 * @param alg :: Shared pointer to the starting algorithm.
 */
void RecordPythonScript::startingHandle(API::IAlgorithm_sptr alg)
{
  auto props= alg->getProperties();

  std::string algString;
  for(auto p = props.begin() ; p != props.end(); ++p)
  {
    std::string opener = "='"; 
    if ((**p).value().find('\\') != std::string::npos )
    {
      opener= "=r'";
    }

    std::string paramString = (**p).name() + opener + (**p).value() + "'";

    // Miss out parameters that are empty.
    if(paramString.length() != 0)
    {
      if(algString.length() != 0)
      {
        algString += ",";
      }
      algString += paramString;
    }
  }

  m_generatedScript +=  alg->name() + "(" + algString + ")\n";
}

/**
 * Removes exponential decay from a workspace
 * @param wsInput :: [input] Workspace to work on
 * @return :: Workspace with decay removed
 */
API::MatrixWorkspace_sptr CalMuonDetectorPhases::removeExpDecay(
    const API::MatrixWorkspace_sptr &wsInput) {
  API::IAlgorithm_sptr remove = createChildAlgorithm("RemoveExpDecay");
  remove->setProperty("InputWorkspace", wsInput);
  remove->executeAsChildAlg();
  API::MatrixWorkspace_sptr wsRem = remove->getProperty("OutputWorkspace");
  return wsRem;
}

/** Call edit instrument geometry
  */
API::MatrixWorkspace_sptr AlignAndFocusPowder::editInstrument(
    API::MatrixWorkspace_sptr ws, std::vector<double> polars,
    std::vector<specnum_t> specids, std::vector<double> l2s,
    std::vector<double> phis) {
  g_log.information() << "running EditInstrumentGeometry started at "
                      << Kernel::DateAndTime::getCurrentTime() << "\n";

  API::IAlgorithm_sptr editAlg = createChildAlgorithm("EditInstrumentGeometry");
  editAlg->setProperty("Workspace", ws);
  if (m_l1 > 0.)
    editAlg->setProperty("PrimaryFlightPath", m_l1);
  if (!polars.empty())
    editAlg->setProperty("Polar", polars);
  if (!specids.empty())
    editAlg->setProperty("SpectrumIDs", specids);
  if (!l2s.empty())
    editAlg->setProperty("L2", l2s);
  if (!phis.empty())
    editAlg->setProperty("Azimuthal", phis);
  editAlg->executeAsChildAlg();

  ws = editAlg->getProperty("Workspace");

  return ws;
}

std::string FrameworkManagerProxy::createAlgorithmDocs(const std::string& algName, const int version)
{
  const std::string EOL="\n";
  API::IAlgorithm_sptr algm = API::AlgorithmManager::Instance().createUnmanaged(algName, version);
  algm->initialize();

  // Put in the quick overview message
  std::stringstream buffer;
  std::string temp = algm->getOptionalMessage();
  if (temp.size() > 0)
    buffer << temp << EOL << EOL;

  // get a sorted copy of the properties
  PropertyVector properties(algm->getProperties());
  std::sort(properties.begin(), properties.end(), PropertyOrdering());

  // generate the sanitized names
  StringVector names(properties.size());
  size_t numProps = properties.size();
  for ( size_t i = 0; i < numProps; ++i) 
  {
    names[i] = removeCharacters(properties[i]->name(), "");
  }

  buffer << "Property descriptions: " << EOL << EOL;
  // write the actual property descriptions
  Mantid::Kernel::Property *prop;
  for ( size_t i = 0; i < numProps; ++i) 
  {
    prop = properties[i];
    buffer << names[i] << "("
           << Mantid::Kernel::Direction::asText(prop->direction());
    if (!prop->isValid().empty())
      buffer << ":req";
    buffer << ") *" << prop->type() << "* ";
    std::set<std::string> allowed = prop->allowedValues();
    if (!prop->documentation().empty() || !allowed.empty())
    {
      buffer << "      " << prop->documentation();
      if (!allowed.empty())
      {
        buffer << " [" << Kernel::Strings::join(allowed.begin(), allowed.end(), ", ");
        buffer << "]";
      }
      buffer << EOL;
      if( i < numProps - 1 ) buffer << EOL;
    }
  }

  return buffer.str();
}

/**
 * Create the concrete instance use for the actual loading.
 * @param startProgress :: The percentage progress value of the overall
 * algorithm where this child algorithm starts
 * @param endProgress :: The percentage progress value of the overall
 * algorithm where this child algorithm ends
 * @param logging :: Set to false to disable logging from the child algorithm
 */
API::IAlgorithm_sptr Load::createLoader(const double startProgress,
                                        const double endProgress,
                                        const bool logging) const {
  std::string name = getPropertyValue("LoaderName");
  int version = getProperty("LoaderVersion");
  API::IAlgorithm_sptr loader =
      API::AlgorithmManager::Instance().createUnmanaged(name, version);
  loader->initialize();
  if (!loader) {
    throw std::runtime_error("Cannot create loader for \"" +
                             getPropertyValue("Filename") + "\"");
  }
  setUpLoader(loader, startProgress, endProgress, logging);
  return loader;
}

/// Run ConvertUnits as a sub-algorithm to convert to dSpacing
MatrixWorkspace_sptr DiffractionFocussing::convertUnitsToDSpacing(const API::MatrixWorkspace_sptr& workspace)
{
  const std::string CONVERSION_UNIT = "dSpacing";

  Unit_const_sptr xUnit = workspace->getAxis(0)->unit();

  g_log.information() << "Converting units from "<< xUnit->label() << " to " << CONVERSION_UNIT<<".\n";

  API::IAlgorithm_sptr childAlg = createSubAlgorithm("ConvertUnits", 0.34, 0.66);
  childAlg->setProperty("InputWorkspace", workspace);
  childAlg->setPropertyValue("Target",CONVERSION_UNIT);
  childAlg->executeAsSubAlg();

  return childAlg->getProperty("OutputWorkspace");
}

/**
 * Declare any additional properties of the concrete loader here
 * @param loader A pointer to the concrete loader
 */
void Load::declareLoaderProperties(const API::IAlgorithm_sptr &loader) {
  // If we have switch loaders then the concrete loader will have different
  // properties
  // so take care of ensuring Load has the correct ones
  // THIS IS A COPY as the properties are mutated as we move through them
  const std::vector<Property *> existingProps = this->getProperties();
  for (auto existingProp : existingProps) {
    const std::string &name = existingProp->name();
    // Wipe all properties except the Load native ones
    if (m_baseProps.find(name) == m_baseProps.end()) {
      this->removeProperty(name);
    }
  }

  const std::vector<Property *> &loaderProps = loader->getProperties();
  size_t numProps(loaderProps.size());
  for (size_t i = 0; i < numProps; ++i) {
    Property *loadProp = loaderProps[i];
    if (loadProp->name() == m_filenamePropName)
      continue;
    try {
      auto propClone = std::unique_ptr<Property>(loadProp->clone());
      propClone->clearSettings(); // Get rid of special settings because it
                                  // does not work in custom GUI.
      declareProperty(std::move(propClone), loadProp->documentation());
    } catch (Exception::ExistsError &) {
      // Already exists as a static property
      continue;
    }
  }
}

void LoadNexusMonitors2::runLoadLogs(const std::string filename,
                                     API::MatrixWorkspace_sptr localWorkspace) {
  // do the actual work
  API::IAlgorithm_sptr loadLogs = createChildAlgorithm("LoadNexusLogs");

  // Now execute the Child Algorithm. Catch and log any error, but don't stop.
  try {
    g_log.information() << "Loading logs from NeXus file..." << std::endl;
    loadLogs->setPropertyValue("Filename", filename);
    loadLogs->setProperty<API::MatrixWorkspace_sptr>("Workspace",
                                                     localWorkspace);
    loadLogs->execute();
  } catch (...) {
    g_log.error() << "Error while loading Logs from Nexus. Some sample logs "
                     "may be missing." << std::endl;
  }
}

/**
 * Set the output workspace(s) if the load's return workspace has type
 * API::Workspace
 * @param loader :: Shared pointer to load algorithm
 */
void Load::setOutputWorkspace(const API::IAlgorithm_sptr &loader) {
  // Go through each OutputWorkspace property and check whether we need to make
  // a counterpart here
  const std::vector<Property *> &loaderProps = loader->getProperties();
  const size_t count = loader->propertyCount();
  for (size_t i = 0; i < count; ++i) {
    Property *prop = loaderProps[i];
    if (dynamic_cast<IWorkspaceProperty *>(prop) &&
        prop->direction() == Direction::Output) {
      const std::string &name = prop->name();
      if (!this->existsProperty(name)) {
        declareProperty(Kernel::make_unique<WorkspaceProperty<Workspace>>(
            name, loader->getPropertyValue(name), Direction::Output));
      }
      Workspace_sptr wkspace = getOutputWorkspace(name, loader);
      setProperty(name, wkspace);
    }
  }
}

/// Run Rebin as a Child Algorithm to harmonise the bin boundaries
void DiffractionFocussing::RebinWorkspace(
    API::MatrixWorkspace_sptr &workspace) {

  double min = 0;
  double max = 0;
  double step = 0;

  calculateRebinParams(workspace, min, max, step);
  std::vector<double> paramArray{min, -step, max};

  g_log.information() << "Rebinning from " << min << " to " << max << " in "
                      << step << " logaritmic steps.\n";

  API::IAlgorithm_sptr childAlg = createChildAlgorithm("Rebin");
  childAlg->setProperty<MatrixWorkspace_sptr>("InputWorkspace", workspace);
  childAlg->setProperty<std::vector<double>>("Params", paramArray);
  childAlg->executeAsChildAlg();
  workspace = childAlg->getProperty("OutputWorkspace");
}

/**
 * Return an output workspace property dealing with the lack of connection
 * between of
 * WorkspaceProperty types
 * @param propName :: The name of the property
 * @param loader :: The loader algorithm
 * @returns A pointer to the OutputWorkspace property of the Child Algorithm
 */
API::Workspace_sptr
Load::getOutputWorkspace(const std::string &propName,
                         const API::IAlgorithm_sptr &loader) const {
  // @todo Need to try and find a better way using the getValue methods
  try {
    return loader->getProperty(propName);
  } catch (std::runtime_error &) {
  }

  // Try a MatrixWorkspace
  try {
    MatrixWorkspace_sptr childWS = loader->getProperty(propName);
    return childWS;
  } catch (std::runtime_error &) {
  }

  // EventWorkspace
  try {
    IEventWorkspace_sptr childWS = loader->getProperty(propName);
    return childWS;
  } catch (std::runtime_error &) {
  }

  // IMDEventWorkspace
  try {
    IMDEventWorkspace_sptr childWS = loader->getProperty(propName);
    return childWS;
  } catch (std::runtime_error &) {
  }

  // General IMDWorkspace
  try {
    IMDWorkspace_sptr childWS = loader->getProperty(propName);
    return childWS;
  } catch (std::runtime_error &) {
  }

  // ITableWorkspace?
  try {
    ITableWorkspace_sptr childWS = loader->getProperty(propName);
    return childWS;
  } catch (std::runtime_error &) {
  }

  // Just workspace?
  try {
    Workspace_sptr childWS = loader->getProperty(propName);
    return childWS;
  } catch (std::runtime_error &) {
  }

  g_log.debug() << "Workspace property " << propName
                << " did not return to MatrixWorkspace, EventWorkspace, "
                   "IMDEventWorkspace, IMDWorkspace\n";
  return Workspace_sptr();
}

void Load::findFilenameProperty(const API::IAlgorithm_sptr &loader) {
  // Use the first file property as the main Filename
  const auto &props = loader->getProperties();
  for (auto prop : props) {
    auto *fp = dynamic_cast<API::MultipleFileProperty *>(prop);
    auto *fp2 = dynamic_cast<API::FileProperty *>(prop);
    if (fp) {
      m_filenamePropName = fp->name();
      break;
    }
    if (fp2) {
      m_filenamePropName = fp2->name();
      break;
    }
  }
  if (m_filenamePropName.empty()) {
    setPropertyValue("LoaderName", "");
    setProperty("LoaderVersion", -1);
    throw std::runtime_error("Cannot find FileProperty on " + loader->name() +
                             " algorithm.");
  }
}

/**
 * Set the loader option for use as a Child Algorithm.
 * @param loader :: Concrete loader
 * @param startProgress :: The start progress fraction
 * @param endProgress :: The end progress fraction
 * @param logging:: If true, enable logging
 */
void Load::setUpLoader(API::IAlgorithm_sptr &loader, const double startProgress,
                       const double endProgress, const bool logging) const {
  // Set as a child so that we are in control of output storage
  loader->setChild(true);
  loader->setLogging(logging);
  // If output workspaces are nameless, give them a temporary name to satisfy
  // validator
  const std::vector<Property *> &props = loader->getProperties();
  for (auto prop : props) {
    auto wsProp = dynamic_cast<IWorkspaceProperty *>(prop);

    if (wsProp && !wsProp->isOptional() &&
        prop->direction() == Direction::Output) {
      if (prop->value().empty())
        prop->setValue("LoadChildWorkspace");
    }
  }
  if (startProgress >= 0. && endProgress > startProgress && endProgress <= 1.) {
    loader->addObserver(this->progressObserver());
    setChildStartProgress(startProgress);
    setChildEndProgress(endProgress);
  }
}

/**  Group detectors in the workspace.
 *  @param ws :: A local workspace
 *  @param spectraList :: A list of spectra to group.
 */
void PlotAsymmetryByLogValue::groupDetectors(API::MatrixWorkspace_sptr& ws,const std::vector<int>& spectraList)
{
    API::IAlgorithm_sptr group = createChildAlgorithm("GroupDetectors");
    group->setProperty("InputWorkspace",ws);
    group->setProperty("SpectraList",spectraList);
    group->setProperty("KeepUngroupedSpectra",true);
    group->execute();
    ws = group->getProperty("OutputWorkspace");
}

/** Rebin
*/
API::MatrixWorkspace_sptr
AlignAndFocusPowder::rebin(API::MatrixWorkspace_sptr matrixws) {
  if (m_resampleX != 0) {
    // ResampleX
    g_log.information() << "running ResampleX(NumberBins=" << abs(m_resampleX)
                        << ", LogBinning=" << (m_resampleX < 0) << ", dMin("
                        << m_dmins.size() << "), dmax(" << m_dmaxs.size()
                        << ")) started at "
                        << Kernel::DateAndTime::getCurrentTime() << "\n";
    API::IAlgorithm_sptr alg = createChildAlgorithm("ResampleX");
    alg->setProperty("InputWorkspace", matrixws);
    alg->setProperty("OutputWorkspace", matrixws);
    if ((!m_dmins.empty()) && (!m_dmaxs.empty())) {
      size_t numHist = m_outputW->getNumberHistograms();
      if ((numHist == m_dmins.size()) && (numHist == m_dmaxs.size())) {
        alg->setProperty("XMin", m_dmins);
        alg->setProperty("XMax", m_dmaxs);
      } else {
        g_log.information()
            << "Number of dmin and dmax values don't match the "
            << "number of workspace indices. Ignoring the parameters.\n";
      }
    }
    alg->setProperty("NumberBins", abs(m_resampleX));
    alg->setProperty("LogBinning", (m_resampleX < 0));
    alg->executeAsChildAlg();
    matrixws = alg->getProperty("OutputWorkspace");
    return matrixws;
  } else {
    g_log.information() << "running Rebin( ";
    for (double param : m_params)
      g_log.information() << param << " ";
    g_log.information() << ") started at "
                        << Kernel::DateAndTime::getCurrentTime() << "\n";
    API::IAlgorithm_sptr rebin3Alg = createChildAlgorithm("Rebin");
    rebin3Alg->setProperty("InputWorkspace", matrixws);
    rebin3Alg->setProperty("OutputWorkspace", matrixws);
    rebin3Alg->setProperty("Params", m_params);
    rebin3Alg->executeAsChildAlg();
    matrixws = rebin3Alg->getProperty("OutputWorkspace");
    return matrixws;
  }
}

/** Extracts relevant data from a workspace
 * @param startTime :: [input] First X value to consider
 * @param endTime :: [input] Last X value to consider
 * @return :: Pre-processed workspace to fit
 */
API::MatrixWorkspace_sptr
CalMuonDetectorPhases::extractDataFromWorkspace(double startTime,
                                                double endTime) {
  // Extract counts from startTime to endTime
  API::IAlgorithm_sptr crop = createChildAlgorithm("CropWorkspace");
  crop->setProperty("InputWorkspace", m_inputWS);
  crop->setProperty("XMin", startTime);
  crop->setProperty("XMax", endTime);
  crop->executeAsChildAlg();
  boost::shared_ptr<API::MatrixWorkspace> wsCrop =
      crop->getProperty("OutputWorkspace");
  return wsCrop;
}

/** Call diffraction focus to a matrix workspace.
  */
API::MatrixWorkspace_sptr
AlignAndFocusPowder::diffractionFocus(API::MatrixWorkspace_sptr ws) {
  if (!m_groupWS) {
    g_log.information() << "not focussing data\n";
    return ws;
  }

  g_log.information() << "running DiffractionFocussing. \n";

  API::IAlgorithm_sptr focusAlg = createChildAlgorithm("DiffractionFocussing");
  focusAlg->setProperty("InputWorkspace", ws);
  focusAlg->setProperty("OutputWorkspace", ws);
  focusAlg->setProperty("GroupingWorkspace", m_groupWS);
  focusAlg->setProperty("PreserveEvents", m_preserveEvents);
  focusAlg->executeAsChildAlg();
  ws = focusAlg->getProperty("OutputWorkspace");

  return ws;
}

void LoadILLSANS::moveDetectorVertical(double shift,
                                       const std::string &componentName) {

  API::IAlgorithm_sptr mover = createChildAlgorithm("MoveInstrumentComponent");
  V3D pos = getComponentPosition(componentName);
  try {
    mover->setProperty<MatrixWorkspace_sptr>("Workspace", m_localWorkspace);
    mover->setProperty("ComponentName", componentName);
    mover->setProperty("X", pos.X());
    mover->setProperty("Y", shift);
    mover->setProperty("Z", pos.Z());
    mover->setProperty("RelativePosition", false);
    mover->executeAsChildAlg();
    g_log.debug() << "Moving component '" << componentName
                  << "' to Y = " << shift << '\n';
  } catch (std::exception &e) {
    g_log.error() << "Cannot move the component '" << componentName
                  << "' to Y = " << shift << '\n';
    g_log.error() << e.what() << '\n';
  }
}