#include "MantidAlgorithms/CalcCountRate.h"

#include "MantidKernel/PropertyWithValue.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/MandatoryValidator.h"

#include "MantidAPI/AlgorithmManager.h"
#include "MantidAPI/Axis.h"

#include "MantidDataObjects/Workspace2D.h"

namespace Mantid {
namespace Algorithms {

// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(CalcCountRate)

//----------------------------------------------------------------------------------------------

/// Algorithms name for identification. @see Algorithm::name
const std::string CalcCountRate::name() const { return "CalcCountRate"; }

/// Algorithm's version for identification. @see Algorithm::version
int CalcCountRate::version() const { return 1; }

/// Algorithm's category for identification. @see Algorithm::category
const std::string CalcCountRate::category() const {
  return "Inelastic\\Utility";
}

/// Algorithm's summary for use in the GUI and help. @see Algorithm::summary
const std::string CalcCountRate::summary() const {
  return "Calculates instrument count rate as the function of the "
         "experiment time and adds CountRate log to the source workspace.";
}

//----------------------------------------------------------------------------------------------
/** Declare the algorithm's properties.
 */
void CalcCountRate::init() {

  declareProperty(
      Kernel::make_unique<API::WorkspaceProperty<DataObjects::EventWorkspace>>(
          "Workspace", "", Kernel::Direction::InOut),
      "Name of the event workspace to calculate counting rate for.");
  declareProperty(Kernel::make_unique<Kernel::PropertyWithValue<double>>(
                      "XMin", EMPTY_DBL(), Kernel::Direction::Input),
                  "Minimal value of X-range for the rate calculations. If left "
                  "to default, Workspace X-axis minimal value is used.");
  declareProperty(Kernel::make_unique<Kernel::PropertyWithValue<double>>(
                      "XMax", EMPTY_DBL(), Kernel::Direction::Input),
                  "Maximal value of X-range for the rate calculations. If left "
                  "to default, Workspace X-axis maximal value is used.");
  declareProperty(
      Kernel::make_unique<Kernel::PropertyWithValue<std::string>>(
          "RangeUnits", "Energy",
          boost::make_shared<Kernel::StringListValidator>(
              Kernel::UnitFactory::Instance().getKeys()),
          Kernel::Direction::Input),
      "The units from Mantid Unit factory for calculating the "
      "counting rate and XMin-XMax ranges are in. If the "
      "X-axis of the input workspace is not expressed"
      "in this units, unit conversion will be performed, so the "
      "workspace should contain all necessary information for this "
      "conversion. E.g. if *RangeUnits* is *EnergyTransfer*, Ei "
      "log containing incident energy value should be attached to the "
      "input workspace.");
  std::vector<std::string> propOptions{"Elastic", "Direct", "Indirect"};
  declareProperty("EMode", "Elastic",
                  boost::make_shared<Kernel::StringListValidator>(propOptions),
                  "The range units above conversion mode (default: elastic)");

  // Used logs group
  std::string used_logs_mode("Used normalization logs");
  declareProperty(
      "NormalizeTheRate", true,
      "Usually you want to normalize counting rate to some "
      "rate related to the source beam intensity. Change this to "
      "'false' if appropriate time series log is broken || not attached to "
      "the input workspace.");
  declareProperty("UseLogDerivative", false, "If the normalization log gives "
                                             "cumulative counting, derivative "
                                             "of this log is necessary to get "
                                             "correct normalization values.");
  declareProperty(
      "NormalizationLogName", "proton_charge",
      "The name of the log, used in the counting rate normalization. ");
  declareProperty(
      "UseNormLogGranularity", true,
      "If true, the calculated log will have the normalization log "
      "accuracy; If false, the 'NumTimeSteps' in the visualization "
      "workspace below will be used for the target log granularity too.");
  setPropertyGroup("NormalizeTheRate", used_logs_mode);
  setPropertyGroup("UseLogDerivative", used_logs_mode);
  setPropertyGroup("NormalizationLogName", used_logs_mode);
  setPropertyGroup("UseNormLogGranularity", used_logs_mode);

  declareProperty(
      "CountRateLogName", "block_count_rate",
      boost::make_shared<Kernel::MandatoryValidator<std::string>>(),
      "The name of the processed time series log with count rate to add"
      " to the source workspace");
  // visualisation group
  std::string spur_vis_mode("Spurion visualisation");
  declareProperty(
      Kernel::make_unique<API::WorkspaceProperty<DataObjects::Workspace2D>>(
          "VisualizationWs", "", Kernel::Direction::Output,
          API::PropertyMode::Optional),
      "Optional name to build 2D matrix workspace for spurion visualization. "
      "If name is provided, a 2D workspace with this name will be created "
      "containing data to visualize counting rate as function of time in the "
      "ranges "
      "XMin-XMax");

  auto mustBeReasonable = boost::make_shared<Kernel::BoundedValidator<int>>();
  mustBeReasonable->setLower(2);
  declareProperty(
      Kernel::make_unique<Kernel::PropertyWithValue<int>>(
          "NumTimeSteps", 200, mustBeReasonable, Kernel::Direction::Input),
      "Number of time steps (time accuracy) the visualization workspace has. "
      "Also number of steps in 'CountRateLogName' log if "
      "'UseNormLogGranularity' is set to false");
  declareProperty(
      Kernel::make_unique<Kernel::PropertyWithValue<int>>(
          "XResolution", 100, mustBeReasonable, Kernel::Direction::Input),
      "Number of steps (accuracy) of the visualization workspace has along "
      "X-axis. ");
  setPropertyGroup("VisualizationWs", spur_vis_mode);
  setPropertyGroup("NumTimeSteps", spur_vis_mode);
  setPropertyGroup("XResolution", spur_vis_mode);
}

//----------------------------------------------------------------------------------------------
/** Execute the algorithm.
 */
void CalcCountRate::exec() {

  DataObjects::EventWorkspace_sptr sourceWS = getProperty("Workspace");

  // Identity correct way to treat input logs and general properties of output
  // log
  this->setOutLogParameters(sourceWS);

  //
  std::string SourceWSName = sourceWS->name();
  if (SourceWSName.size() == 0) {
    SourceWSName = "CalcCountRateInputWS";
  }
  // Sum spectra of the input workspace
  auto summator = createChildAlgorithm("SumSpectra", 0, 1);
  summator->setProperty("InputWorkspace", sourceWS);
  summator->setProperty("OutputWorkspace", "__" + SourceWSName + "_Sum");
  summator->setProperty("IncludeMonitors", false);

  summator->execute();

  API::MatrixWorkspace_sptr source = summator->getProperty("OutputWorkspace");
  m_workingWS =
      boost::dynamic_pointer_cast<DataObjects::EventWorkspace>(source);
  if (!m_workingWS) {
    throw std::invalid_argument(
        "Can not sum spectra of input event workspace: " + sourceWS->name());
  }
  //-------------------------------------
  // identify ranges for count rate calculations
  this->setWSDataRanges(m_workingWS);

  // create results log and add it to the source workspace
  std::string logname = getProperty("CountRateLogName");
  auto newlog = new Kernel::TimeSeriesProperty<double>(logname);
  sourceWS->mutableRun().addProperty(newlog, true);

  // calculate averages requested and modify results log
  this->calcRateLog(m_workingWS,newlog);


  // clear up log derivative and existing log pointer (if any)
  // to avoid incorrect usage
  // at subsequent calls to the same algorithm.
  m_logDerivHolder.release();
  m_pNormalizationLog = nullptr;

  /*

  auto newlog = new TimeSeriesProperty<double>(logname);
  newlog->setUnits(oldlog->units());
  int size = oldlog->realSize();
  vector<double> values = oldlog->valuesAsVector();
  vector<DateAndTime> times = oldlog->timesAsVector();
  for (int i = 0; i < size; i++) {
  newlog->addValue(times[i] + offset, values[i]);
  }

  // Just overwrite if the change is in place
  MatrixWorkspace_sptr outputWS = getProperty("OutputWorkspace");
  if (outputWS != inputWS) {
  IAlgorithm_sptr duplicate = createChildAlgorithm("CloneWorkspace");
  duplicate->initialize();
  duplicate->setProperty<Workspace_sptr>(
  "InputWorkspace", boost::dynamic_pointer_cast<Workspace>(inputWS));
  duplicate->execute();
  Workspace_sptr temp = duplicate->getProperty("OutputWorkspace");
  outputWS = boost::dynamic_pointer_cast<MatrixWorkspace>(temp);

  setProperty("OutputWorkspace", outputWS);
  }

  outputWS->mutableRun().addProperty(newlog, true);

    */
}
void CalcCountRate::calcRateLog(DataObjects::EventWorkspace_sptr &InputWorkspace,
    Kernel::TimeSeriesProperty<double> *const targLog) {

}

/*Analyse input log parameters and logs, attached to the workspace and identify
 * the parameters of the target log
 @param InputWorkspace -- input workspace to analyse logs
 */
void CalcCountRate::setOutLogParameters(
    const DataObjects::EventWorkspace_sptr &InputWorkspace) {

  std::string NormLogName = getProperty("NormalizationLogName");

  bool normalizeResult = getProperty("NormalizeTheRate");
  bool useLogDerivative = getProperty("UseLogDerivative");
  bool useLogAccuracy = getProperty("UseNormLogGranularity");

  bool logPresent = InputWorkspace->run().hasProperty(NormLogName);
  if (!logPresent) {
    if (normalizeResult) {
      g_log.warning() << "Normalization by log " << NormLogName
                      << " values requested but the log is not attached to the "
                         "workspace. Normalization disabled\n";
      normalizeResult = false;
    }
    if (useLogDerivative) {
      g_log.warning() << "Normalization by log " << NormLogName
                      << " derivative requested but the log is not attached to "
                         "the workspace. Normalization disabled\n";
      useLogDerivative = false;
    }
    if (useLogAccuracy) {
      g_log.warning() << "Using accuracy of the log " << NormLogName
                      << " is requested but the log is not attached to the "
                         "workspace. Will use accuracy defined by "
                         "'NumTimeSteps' property value\n";
      useLogAccuracy = false;
    }
  } else {
    m_pNormalizationLog =
        InputWorkspace->run().getTimeSeriesProperty<double>(NormLogName);
  }

  // Analyse properties interactions

  // if property derivative is specified.
  if (useLogDerivative) {
    m_logDerivHolder = m_pNormalizationLog->getDerivative();
    m_pNormalizationLog = m_logDerivHolder.get();
  }

  ///
  if (useLogAccuracy) {
    m_numLogSteps = m_pNormalizationLog->realSize();
  } else {
    m_numLogSteps = getProperty("NumTimeSteps");
  }
}

/* Retrieve and define data search ranges from input workspace parameters and
 * algorithm properties
 *
 *@param InputWorkspace -- event workspace to process. Also retrieves algorithm
 *                         properties, relevant to the workspace.
 *@return -- the input workspace cropped according to XMin-XMax ranges in units,
 *           requested by the user
 *
*/
void CalcCountRate::setWSDataRanges(
    DataObjects::EventWorkspace_sptr &InputWorkspace) {
  m_XRangeMin = getProperty("XMin");
  m_XRangeMax = getProperty("XMax");

  if (m_XRangeMin == EMPTY_DBL() && m_XRangeMax == EMPTY_DBL()) {
    m_rangeExplicit = false;
  } else {
    m_rangeExplicit = true;
  }
  if (!m_rangeExplicit) {
    InputWorkspace->getEventXMinMax(m_XRangeMin, m_XRangeMax);
    return;
  }
  // Search within partial range;
  std::string RangeUnits = getProperty("RangeUnits");
  auto axis = InputWorkspace->getAxis(0);
  const auto unit = axis->unit();

  API::MatrixWorkspace_sptr wst;
  std::string wsName = InputWorkspace->name();
  if (wsName.size() == 0) {
    wsName = "_CropDataWS";
  }

  if (unit->unitID() != RangeUnits) {
    auto conv = createChildAlgorithm("ConvertUnits", 0, 1);

    conv->setProperty("InputWorkspace", InputWorkspace);
    conv->setPropertyValue("OutputWorkspace", wsName);
    std::string Emode = getProperty("Emode");
    conv->setProperty("Emode", Emode);
    conv->setProperty("Target", RangeUnits);

    conv->execute();
    wst = conv->getProperty("OutputWorkspace");

  } else {
    wst = InputWorkspace;
  }
  auto wste = boost::dynamic_pointer_cast<DataObjects::EventWorkspace>(wst);
  if (!wste) {
    throw std::runtime_error("SetWSDataRanges:Can not retrieve EventWorkspace "
                             "after converting units");
  }
  // here the ranges have been changed so both will newer remain defaults
  double realMin, realMax;
  wste->getEventXMinMax(realMin, realMax);

  if (m_XRangeMin == EMPTY_DBL()) {
    m_XRangeMin = realMin;
  }
  if (m_XRangeMax == EMPTY_DBL()) {
    m_XRangeMax = realMax;
  }
  if (m_XRangeMin < realMin) {
    g_log.debug() << "Workspace constrain min range changed from: "
                  << m_XRangeMin << " To: " << realMin << std::endl;
    m_XRangeMin = realMin;
  }
  if (m_XRangeMax > realMax) {
    g_log.debug() << "Workspace constrain max range changed from: "
                  << m_XRangeMax << " To: " << realMax << std::endl;
    m_XRangeMax = realMax;
  }

  //
  auto crop = createChildAlgorithm("CropWorkspace", 0, 1);
  crop->setProperty("InputWorkspace", wste);
  crop->setProperty("OutputWorkspace", wsName);
  crop->setProperty("XMin", m_XRangeMin);
  crop->setProperty("XMax", m_XRangeMax);

  crop->execute();

  wst = crop->getProperty("OutputWorkspace");

  InputWorkspace =
      boost::dynamic_pointer_cast<DataObjects::EventWorkspace>(wst);
  if (!InputWorkspace) {
    throw std::runtime_error(
        "Can not crop input workspace within the XMin-XMax ranges requested");
  }
}
/** Helper function, mainly for testing
* @return  true if count rate should be normalized and false
* otherwise */
bool CalcCountRate::notmalizeCountRate() const {
  return (m_pNormalizationLog != nullptr);
}
/** Helper function, mainly for testing
* @return  true if log derivative is used instead of log itself */
bool CalcCountRate::useLogDerivative() const { return bool(m_logDerivHolder); }

} // namespace Algorithms
} // namespace Mantid