#include "MantidAlgorithms/CalculateZscore.h"

#include "MantidAPI/WorkspaceProperty.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/Statistics.h"
#include "MantidDataObjects/Workspace2D.h"

#include <sstream>

using namespace Mantid;
using namespace Mantid::API;
using namespace Mantid::Kernel;
using namespace Mantid::DataObjects;
using namespace std;

namespace Mantid {
namespace Algorithms {

DECLARE_ALGORITHM(CalculateZscore)

//----------------------------------------------------------------------------------------------
/** Constructor
 */
CalculateZscore::CalculateZscore() {}

//----------------------------------------------------------------------------------------------
/** Destructor
 */
CalculateZscore::~CalculateZscore() {}

//----------------------------------------------------------------------------------------------
/** Define properties
  */
void CalculateZscore::init() {
  auto inwsprop = new WorkspaceProperty<MatrixWorkspace>(
      "InputWorkspace", "Anonymous", Direction::Input);
  declareProperty(inwsprop,
                  "Name of input MatrixWorkspace to have Z-score calculated.");

  auto outwsprop = new WorkspaceProperty<Workspace2D>("OutputWorkspace", "",
                                                      Direction::Output);
  declareProperty(outwsprop,
                  "Name of the output Workspace2D containing the Z-scores.");

  declareProperty("WorkspaceIndex", EMPTY_INT(),
                  "Index of the spetrum to have Z-score calculated. "
                  "Default is to calculate for all spectra.");
}

//----------------------------------------------------------------------------------------------
/** Execute body
  */
void CalculateZscore::exec() {
  // 1. Get input and validate
  MatrixWorkspace_const_sptr inpWS = getProperty("InputWorkspace");
  int inpwsindex = getProperty("WorkspaceIndex");

  bool zscoreforall = false;
  if (inpwsindex == EMPTY_INT()) {
    zscoreforall = true;
  }

  // 2. Generate output
  size_t numspec;
  if (zscoreforall) {
    numspec = inpWS->getNumberHistograms();
  } else {
    numspec = 1;
  }
  size_t sizex = inpWS->readX(0).size();
  size_t sizey = inpWS->readY(0).size();

  Workspace2D_sptr outWS = boost::dynamic_pointer_cast<Workspace2D>(
      WorkspaceFactory::Instance().create("Workspace2D", numspec, sizex,
                                          sizey));

  Progress progress(this, 0, 1, numspec);

  // 3. Get Z values
  for (size_t i = 0; i < numspec; ++i) {
    // a) figure out wsindex
    size_t wsindex;
    if (zscoreforall) {
      // Update wsindex to index in input workspace
      wsindex = i;
    } else {
      // Use the wsindex as the input
      wsindex = static_cast<size_t>(inpwsindex);
      if (wsindex >= inpWS->getNumberHistograms()) {
        stringstream errmsg;
        errmsg << "Input workspace index " << inpwsindex
               << " is out of input workspace range = "
               << inpWS->getNumberHistograms() << endl;
      }
    }

    // b) Calculate Zscore
    const MantidVec &inpX = inpWS->readX(wsindex);
    const MantidVec &inpY = inpWS->readY(wsindex);
    const MantidVec &inpE = inpWS->readE(wsindex);

    MantidVec &vecX = outWS->dataX(i);
    MantidVec &vecY = outWS->dataY(i);
    MantidVec &vecE = outWS->dataE(i);

    vector<double> yzscores = getZscore(inpY);
    vector<double> ezscores = getZscore(inpE);

    vecX = inpX;
    vecY = yzscores;
    vecE = ezscores;

    progress.report("Calculating Z Score");
  } // ENDFOR

  // 4. Set the output
  setProperty("OutputWorkspace", outWS);

  return;
}

} // namespace Algorithms
} // namespace Mantid