Rebin.cpp

//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
#include "MantidAlgorithms/Rebin.h"

#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/VectorHelper.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/RebinParamsValidator.h"
#include "MantidKernel/VisibleWhenProperty.h"

#include "MantidAPI/WorkspaceValidators.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/EventList.h"


namespace Mantid
{
  namespace Algorithms
  {

    // Register the class into the algorithm factory
    DECLARE_ALGORITHM(Rebin)

    using namespace Kernel;
    using namespace API;
    using DataObjects::EventList;
    using DataObjects::EventWorkspace;
    using DataObjects::EventWorkspace_sptr;
    using DataObjects::EventWorkspace_const_sptr;

    //---------------------------------------------------------------------------------------------
    // Public static methods
    //---------------------------------------------------------------------------------------------

    /**
    * Return the rebin parameters from a user input
    * @param inParams Input vector from user
    * @param inputWS Input workspace from user
    * @param logger A reference to a logger
    * @returns A new vector containing the rebin parameters
    */
    std::vector<double> Rebin::rebinParamsFromInput(const std::vector<double> & inParams,
      const API::MatrixWorkspace & inputWS,
      Kernel::Logger & logger)
    {
      std::vector<double> rbParams;
      // The validator only passes parameters with size 1, or 3xn.  No need to check again here
      if (inParams.size() >= 3)
      {
        // Input are min, delta, max
        rbParams = inParams;
      }
      else if (inParams.size() == 1)
      {
        double xmin = 0.;
        double xmax = 0.;
        inputWS.getXMinMax(xmin, xmax);

        logger.information() << "Using the current min and max as default " << xmin << ", " << xmax << std::endl;
        rbParams.resize(3);
        rbParams[0] = xmin;
        rbParams[1] = inParams[0];
        rbParams[2] = xmax;
      }
      return rbParams;
    }

    //---------------------------------------------------------------------------------------------
    // Public methods
    //---------------------------------------------------------------------------------------------

    /** Initialisation method. Declares properties to be used in algorithm.
    *
    */
    void Rebin::init()
    {
      declareProperty(
        new WorkspaceProperty<>("InputWorkspace", "", Direction::Input),
        "Workspace containing the input data");
      declareProperty(
        new WorkspaceProperty<>("OutputWorkspace","",Direction::Output),
        "The name to give the output workspace");

      declareProperty(
        new ArrayProperty<double>("Params", boost::make_shared<RebinParamsValidator>()),
        "A comma separated list of first bin boundary, width, last bin boundary. Optionally "
        "this can be followed by a comma and more widths and last boundary pairs. "
        "Optionally this can also be a single number, which is the bin width. "
        "In this case, the boundary of binning will be determined by minimum and maximum TOF "
        "values among all events, or previous binning boundary, in case of event Workspace, or "
        "non-event Workspace, respectively. Negative width values indicate logarithmic binning. ");

      declareProperty("PreserveEvents", true,"Keep the output workspace as an EventWorkspace, "
        "if the input has events. If the input and output EventWorkspace "
        "names are the same, only the X bins are set, which is very quick. If false, "
        "then the workspace gets converted to a Workspace2D histogram.");

      declareProperty("FullBinsOnly", false, "Omit the final bin if it's width is smaller than the step size");
      //---------------------------------------------------------------
      // 
      auto vsValidator = boost::make_shared<CompositeValidator>();
      vsValidator->add<InstrumentValidator>();
      vsValidator->add<WorkspaceUnitValidator>("TOF");
      vsValidator->add<HistogramValidator>();
      declareProperty(new WorkspaceProperty<>("FlatBkgWorkspace","",Direction::Input,API::PropertyMode::Optional,vsValidator),
        "An optional histogram workspace in the units of TOF defining background for removal during rebinning."
        "The workspace has to have single value or contain the same number of spectra as the \"InputWorkspace\" and single Y value per each spectra," 
        "representing flat background in the background time region. "
        "If such workspace is present, the value of the flat background provided by this workspace is removed "
        "from each spectra of the rebinned workspace. This works for histogram and event workspace when events are not retained "
        "but actually useful mainly for removing background while rebinning an event workspace in the units different from TOF.");

      std::vector<std::string> dE_modes = Kernel::DeltaEMode().availableTypes();
      declareProperty("EMode",dE_modes[Kernel::DeltaEMode::Direct],boost::make_shared<Kernel::StringListValidator>(dE_modes),
        "If FlatBkgWorkspace is present, this property used to define the units conversion from TOF to the units of the InputWorkspace",Direction::Input);
      setPropertySettings("EMode",
        new Kernel::VisibleWhenProperty("FlatBkgWorkspace", IS_NOT_EQUAL_TO, ""));

      std::string bgRemovalGrp("Remove Background during rebinning settings:");
      setPropertyGroup("FlatBkgWorkspace", bgRemovalGrp);
      setPropertyGroup("EMode", bgRemovalGrp);
    }


    /** Executes the rebin algorithm
    *
    *  @throw runtime_error Thrown if the bin range does not intersect the range of the input workspace
    */
    void Rebin::exec()
    {
      // Get the input workspace
      MatrixWorkspace_sptr inputWS = getProperty("InputWorkspace");
      MatrixWorkspace_sptr outputWS = getProperty("OutputWorkspace");

      // Are we preserving event workspace-iness?
      bool PreserveEvents = getProperty("PreserveEvents");

      // Rebinning in-place
      bool inPlace = (inputWS == outputWS);

      std::vector<double> rbParams = rebinParamsFromInput(getProperty("Params"), *inputWS, g_log);

      const bool dist = inputWS->isDistribution();
      const bool isHist = inputWS->isHistogramData();

      // workspace independent determination of length
      const int histnumber = static_cast<int>(inputWS->getNumberHistograms());

      //-- Flat Background removal ----------------------------
      int eMode; // in convert units emode is still integer
      API::MatrixWorkspace_const_sptr bkgWS = checkRemoveBackgroundParameters(inputWS,eMode,PreserveEvents);
      const bool remove_background = bool(bkgWS);
      if(remove_background)
        m_BackgroundHelper.initialize(bkgWS,inputWS,eMode);
      //-------------------------------------------------------

      bool fullBinsOnly = getProperty("FullBinsOnly");

      MantidVecPtr XValues_new;
      // create new output X axis
      const int ntcnew = VectorHelper::createAxisFromRebinParams(rbParams, XValues_new.access(),
        true, fullBinsOnly);

      //---------------------------------------------------------------------------------
      //Now, determine if the input workspace is actually an EventWorkspace
      EventWorkspace_const_sptr eventInputWS = boost::dynamic_pointer_cast<const EventWorkspace>(inputWS);

      if (eventInputWS != NULL)
      {
        //------- EventWorkspace as input -------------------------------------
        EventWorkspace_sptr eventOutputWS = boost::dynamic_pointer_cast<EventWorkspace>(outputWS);

        if (inPlace && PreserveEvents)
        {
          // -------------Rebin in-place, preserving events ----------------------------------------------
          // This only sets the X axis. Actual rebinning will be done upon data access.
          eventOutputWS->setAllX(XValues_new);
          this->setProperty("OutputWorkspace", boost::dynamic_pointer_cast<MatrixWorkspace>(eventOutputWS));
        }
        else if (!inPlace && PreserveEvents)
        {
          // -------- NOT in-place, but you want to keep events for some reason. ----------------------
          // Must copy the event workspace to a new EventWorkspace (and bin that).

          //Make a brand new EventWorkspace
          eventOutputWS = boost::dynamic_pointer_cast<EventWorkspace>(
            API::WorkspaceFactory::Instance().create("EventWorkspace", inputWS->getNumberHistograms(), 2, 1));
          //Copy geometry over.
          API::WorkspaceFactory::Instance().initializeFromParent(inputWS, eventOutputWS, false);
          //You need to copy over the data as well.
          eventOutputWS->copyDataFrom( (*eventInputWS) );

          // This only sets the X axis. Actual rebinning will be done upon data access.
          eventOutputWS->setAllX(XValues_new);

          //Cast to the matrixOutputWS and save it
          this->setProperty("OutputWorkspace", boost::dynamic_pointer_cast<MatrixWorkspace>(eventOutputWS));
        }
        else
        {
          //--------- Different output, OR you're inplace but not preserving Events --- create a Workspace2D -------
          g_log.information() << "Creating a Workspace2D from the EventWorkspace " << eventInputWS->getName() << ".\n";

          //Create a Workspace2D
          // This creates a new Workspace2D through a torturous route using the WorkspaceFactory.
          // The Workspace2D is created with an EMPTY CONSTRUCTOR
          outputWS = WorkspaceFactory::Instance().create("Workspace2D",histnumber,ntcnew,ntcnew-1);
          WorkspaceFactory::Instance().initializeFromParent(inputWS, outputWS, true);

          //Initialize progress reporting.
          Progress prog(this,0.0,1.0, histnumber);

          //Go through all the histograms and set the data
          PARALLEL_FOR3(inputWS, eventInputWS, outputWS)
            for (int i=0; i < histnumber; ++i)
            {
              PARALLEL_START_INTERUPT_REGION

                //Set the X axis for each output histogram
                outputWS->setX(i, XValues_new);

              //Get a const event list reference. eventInputWS->dataY() doesn't work.
              const EventList& el = eventInputWS->getEventList(i);
              MantidVec y_data, e_data;
              // The EventList takes care of histogramming.
              el.generateHistogram(*XValues_new, y_data, e_data);
              if(remove_background)
              {
                m_BackgroundHelper.removeBackground(i,*XValues_new,y_data,e_data);
              }


              //Copy the data over.
              outputWS->dataY(i).assign(y_data.begin(), y_data.end());
              outputWS->dataE(i).assign(e_data.begin(), e_data.end());

              //Report progress
              prog.report(name());
              PARALLEL_END_INTERUPT_REGION
            }
            PARALLEL_CHECK_INTERUPT_REGION


              //Copy all the axes
              for (int i=1; i<inputWS->axes(); i++)
              {
                outputWS->replaceAxis( i, inputWS->getAxis(i)->clone(outputWS.get()) );
                outputWS->getAxis(i)->unit() = inputWS->getAxis(i)->unit();
              }

              //Copy the units over too.
              for (int i=0; i < outputWS->axes(); ++i)
                outputWS->getAxis(i)->unit() = inputWS->getAxis(i)->unit();
              outputWS->setYUnit(eventInputWS->YUnit());
              outputWS->setYUnitLabel(eventInputWS->YUnitLabel());

              // Assign it to the output workspace property
              setProperty("OutputWorkspace", outputWS);
        }

      } // END ---- EventWorkspace

      else

      { //------- Workspace2D or other MatrixWorkspace ---------------------------

        if ( ! isHist )
        {
          g_log.information() << "Rebin: Converting Data to Histogram." << std::endl;
          Mantid::API::Algorithm_sptr ChildAlg = createChildAlgorithm("ConvertToHistogram");
          ChildAlg->initialize();
          ChildAlg->setProperty("InputWorkspace", inputWS);
          ChildAlg->execute();
          inputWS = ChildAlg->getProperty("OutputWorkspace");
        }

        // This will be the output workspace (exact type may vary)
        API::MatrixWorkspace_sptr outputWS;

        // make output Workspace the same type is the input, but with new length of signal array
        outputWS = API::WorkspaceFactory::Instance().create(inputWS,histnumber,ntcnew,ntcnew-1);


        // Copy over the 'vertical' axis
        if (inputWS->axes() > 1) outputWS->replaceAxis( 1, inputWS->getAxis(1)->clone(outputWS.get()) );

        Progress prog(this,0.0,1.0,histnumber);
        PARALLEL_FOR2(inputWS,outputWS)
          for (int hist=0; hist <  histnumber;++hist)
          {
            PARALLEL_START_INTERUPT_REGION
              // get const references to input Workspace arrays (no copying)
              const MantidVec& XValues = inputWS->readX(hist);
            const MantidVec& YValues = inputWS->readY(hist);
            const MantidVec& YErrors = inputWS->readE(hist);

            //get references to output workspace data (no copying)
            MantidVec& YValues_new=outputWS->dataY(hist);
            MantidVec& YErrors_new=outputWS->dataE(hist);

            // output data arrays are implicitly filled by function
            try {
              VectorHelper::rebin(XValues,YValues,YErrors,*XValues_new,YValues_new,YErrors_new, dist);
              if(remove_background)
              {
                m_BackgroundHelper.removeBackground(hist,*XValues_new,YValues_new,YErrors_new);
              }
            } catch (std::exception& ex)
            {
              g_log.error() << "Error in rebin function: " << ex.what() << std::endl;
              throw;
            }

            // Populate the output workspace X values
            outputWS->setX(hist,XValues_new);

            prog.report(name());
            PARALLEL_END_INTERUPT_REGION
          }
          PARALLEL_CHECK_INTERUPT_REGION
            outputWS->isDistribution(dist);

          // Now propagate any masking correctly to the output workspace
          // More efficient to have this in a separate loop because
          // MatrixWorkspace::maskBins blocks multi-threading
          for (int i=0; i <  histnumber; ++i)
          {
            if ( inputWS->hasMaskedBins(i) )  // Does the current spectrum have any masked bins?
            {
              this->propagateMasks(inputWS,outputWS,i);
            }
          }
          //Copy the units over too.
          for (int i=0; i < outputWS->axes(); ++i)
          {
            outputWS->getAxis(i)->unit() = inputWS->getAxis(i)->unit();
          }

          if ( ! isHist )
          {
            g_log.information() << "Rebin: Converting Data back to Data Points." << std::endl;
            Mantid::API::Algorithm_sptr ChildAlg = createChildAlgorithm("ConvertToPointData");
            ChildAlg->initialize();
            ChildAlg->setProperty<MatrixWorkspace_sptr>("InputWorkspace", outputWS);
            ChildAlg->execute();
            outputWS = ChildAlg->getProperty("OutputWorkspace");
          }

          if(remove_background)
          {
            const std::list<int> &failedBkgRemoalList= m_BackgroundHelper.getFailingSpectrsList();
            if(!failedBkgRemoalList.empty())
            {
              size_t nFailed = failedBkgRemoalList.size();
              if(nFailed == static_cast<size_t>(histnumber))
              {
                g_log.warning()<<" has not been able to remove any background while rebinning workspace "<<inputWS->getName()<<
                  "\n possible reasons: wrong instrument or units conversion mode\n";
              }
              else
              {
                g_log.debug()<<" has not removed background from  "<<nFailed<<" spectra\n";
                if(nFailed<20)
                {
                  g_log.debug()<<" Spectra numbers are: ";
                  for(auto it=failedBkgRemoalList.begin(); it !=failedBkgRemoalList.end();it++) g_log.debug()<<(*it);
                  g_log.debug()<<"\n";
                }
              }
            }
          }


          // Assign it to the output workspace property
          setProperty("OutputWorkspace",outputWS);


      } // END ---- Workspace2D

      return;
    }
    /*** method checks if removing background is requested and possible 
    and if yes sets up class parameter referring the workspace with flat background 

    @param inputWS the input workspace where removing background is expected
    @param eMode   the energy conversion mode, defined/requested for the instrument

    @returns background  workspace if removal is expected
    */
    API::MatrixWorkspace_const_sptr Rebin::checkRemoveBackgroundParameters(const API::MatrixWorkspace_sptr &inputWS,int &eMode, bool PreserveEvents)
    {
      API::MatrixWorkspace_const_sptr bkgWksp = getProperty("FlatBkgWorkspace");

      if (!bkgWksp)
        return bkgWksp;

      // can not remove background while preserving events
      if(PreserveEvents)
        return API::MatrixWorkspace_const_sptr();

      // source workspace has to have full instrument defined to perform background removal using this procedure. 
      auto pInstrument = inputWS->getInstrument();
      if(pInstrument)
      {
        if(!pInstrument->getSample())
        {
          g_log.warning()<<" Workspace: "<< inputWS->getName()<< " to rebin does not have properly defined instrument. Background removal will not be performed";
          return API::MatrixWorkspace_const_sptr();
        }

      }
      else
      {
        g_log.warning()<<" Workspace: "<< inputWS->getName()<< " to rebin does not have instrument attached. Background removal will not be performed";
        return API::MatrixWorkspace_const_sptr();
      }

      if(!(bkgWksp->getNumberHistograms() == 1 || inputWS->getNumberHistograms()==bkgWksp->getNumberHistograms()))
      {
        g_log.warning()<<" Background Workspace: "<< bkgWksp->getName()<< " should have the same number of spectra as source workspace or be a single histogram workspace\n";
        return API::MatrixWorkspace_const_sptr();
      }


      const std::string emodeStr = getProperty("EMode");
      eMode = static_cast<int>(Kernel::DeltaEMode().fromString(emodeStr));

      return bkgWksp;
    }


    //
    //    /** Continue execution for EventWorkspace scenario */
    //    void Rebin::execEvent()
    //    {
    //      // retrieve the properties
    //      std::vector<double> rb_params=getProperty("Params");
    //
    //    }

    /** Takes the masks in the input workspace and apportions the weights into the new bins that overlap
    *  with a masked bin. These bins are then masked with the calculated weight.
    * 
    *  @param inputWS ::  The input workspace
    *  @param outputWS :: The output workspace
    *  @param hist ::    The index of the current histogram
    */
    void Rebin::propagateMasks(API::MatrixWorkspace_const_sptr inputWS, API::MatrixWorkspace_sptr outputWS, int hist)
    {
      // Not too happy with the efficiency of this way of doing it, but it's a lot simpler to use the
      // existing rebin algorithm to distribute the weights than to re-implement it for this

      MantidVec masked_bins,weights;
      // Get a reference to the list of masked bins for this spectrum
      const MatrixWorkspace::MaskList& mask = inputWS->maskedBins(hist);
      // Now iterate over the list, building up a vector of the masked bins
      MatrixWorkspace::MaskList::const_iterator it = mask.begin();
      const MantidVec& XValues = inputWS->readX(hist);
      masked_bins.push_back(XValues[(*it).first]);
      weights.push_back((*it).second);
      masked_bins.push_back(XValues[(*it).first + 1]);
      for (++it; it!= mask.end(); ++it)
      {
        const double currentX = XValues[(*it).first];
        // Add an intermediate bin with zero weight if masked bins aren't consecutive
        if (masked_bins.back() != currentX) 
        {
          weights.push_back(0.0);
          masked_bins.push_back(currentX);
        }
        weights.push_back((*it).second);
        masked_bins.push_back(XValues[(*it).first + 1]);
      }

      // Create a zero vector for the errors because we don't care about them here
      const MantidVec zeroes(weights.size(),0.0);
      // Create a vector to hold the redistributed weights
      const MantidVec& XValues_new = outputWS->readX(hist);
      MantidVec newWeights(XValues_new.size()-1),zeroes2(XValues_new.size()-1);
      // Use rebin function to redistribute the weights. Note that distribution flag is set
      VectorHelper::rebin(masked_bins,weights,zeroes,XValues_new,newWeights,zeroes2,true);

      // Now process the output vector and fill the new masking list
      for (size_t index = 0; index < newWeights.size(); ++index)
      {
        if ( newWeights[index] > 0.0 ) outputWS->flagMasked(hist, index, newWeights[index]);
      }
    }

  } // namespace Algorithm
} // namespace Mantid