PeaksWorkspace.cpp 15.1 KB
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#include "MantidAPI/AlgorithmFactory.h"
#include "MantidAPI/Column.h"
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#include "MantidAPI/ColumnFactory.h"
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#include "MantidAPI/MatrixWorkspace.h"
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#include "MantidNexusCPP/NeXusFile.hpp"
#include "MantidNexusCPP/NeXusException.hpp"
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#include "MantidAPI/WorkspaceFactory.h"
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#include "MantidAPI/WorkspaceProperty.h"
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#include "MantidDataObjects/PeaksWorkspace.h"
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#include "MantidDataObjects/TableColumn.h"
#include "MantidDataObjects/TableWorkspace.h"
#include "MantidDataObjects/Peak.h"
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#include "MantidKernel/Quat.h"
#include "MantidKernel/V3D.h"
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#include "MantidKernel/DateAndTime.h"
#include "MantidKernel/Logger.h"
#include "MantidKernel/PhysicalConstants.h"
#include "MantidKernel/Unit.h"
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#include <algorithm>
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#include <boost/shared_ptr.hpp>
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#include <exception>
#include <fstream>
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#include <iostream>
#include <math.h>
#include <ostream>
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#include <stdio.h>
#include <stdlib.h>
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#include <string>

using namespace Mantid::API;
using namespace Mantid::Kernel;
using namespace Mantid::Geometry;
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namespace Mantid
{
namespace DataObjects
{
  /// Register the workspace as a type
  DECLARE_WORKSPACE(PeaksWorkspace );

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//  Kernel::Logger& PeaksWorkspace::g_log = Kernel::Logger::get("PeaksWorkspace");
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  //---------------------------------------------------------------------------------------------
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  /** Constructor. Create a table with all the required columns.
   *
   * @return PeaksWorkspace object
   */
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  PeaksWorkspace::PeaksWorkspace()
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  : IPeaksWorkspace()
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  {
    initColumns();
  }

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  //---------------------------------------------------------------------------------------------
  /** Virtual constructor. Clone method to duplicate the peaks workspace.
   *
   * @return PeaksWorkspace object
   */
  PeaksWorkspace* PeaksWorkspace::clone() const
  {
    //Deep copy via copy construtor.
    return new PeaksWorkspace(*this);
  }

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  //---------------------------------------------------------------------------------------------
  /** Copy constructor
   *
   * @param other :: other PeaksWorkspace to copy from
   * @return
   */
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  PeaksWorkspace::PeaksWorkspace(const PeaksWorkspace & other)
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  : IPeaksWorkspace(other),
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    peaks(other.peaks)
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  {
    initColumns();
    this->peaks = other.peaks;
  }

  //---------------------------------------------------------------------------------------------
  /** Clone a shared pointer
   *
   * @param other :: other PeaksWorkspace to copy from
   * @return copy of the peaksworkspace
   */
  boost::shared_ptr<PeaksWorkspace> PeaksWorkspace::clone()
  {
    // Copy construct and return
    return boost::shared_ptr<PeaksWorkspace>(new PeaksWorkspace(*this));
  }

  //---------------------------------------------------------------------------------------------
  /** Initialize all columns */
  void PeaksWorkspace::initColumns()
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  {
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    // Note: These column names must match what PeakColumn expects!
    addColumn( "int", "RunNumber");
    addColumn( "int", "DetID");
    addColumn( "double", "h");
    addColumn( "double", "k");
    addColumn( "double", "l");
    addColumn( "double", "Wavelength");
    addColumn( "double", "Energy");
    addColumn( "double", "TOF");
    addColumn( "double", "DSpacing");
    addColumn( "double", "Intens");
    addColumn( "double", "SigInt");
    addColumn( "double", "BinCount");
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    addColumn( "str", "BankName");
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    addColumn( "double", "Row");
    addColumn( "double", "Col");
    addColumn( "V3D", "QLab");
    addColumn( "V3D", "QSample");
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  }

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  //=====================================================================================
  //=====================================================================================
  /** Comparator class for sorting peaks by one or more criteria
   */
  class PeakComparator : public std::binary_function<Peak,Peak,bool>
  {
  public:
    std::vector< std::pair<std::string, bool> > & criteria;

    /** Constructor for the comparator for sorting peaks
    * @param criteria : a vector with a list of pairs: column name, bool;
    *        where bool = true for ascending, false for descending sort.
    */
    PeakComparator(std::vector< std::pair<std::string, bool> > & criteria)
    : criteria(criteria)
    {
    }

    /** Compare two peaks using the stored criteria */
    inline bool operator()(const Peak& a, const Peak& b)
    {
      for (size_t i = 0; i < criteria.size(); i++)
      {
        std::string & col = criteria[i].first;
        bool ascending = criteria[i].second;
        bool lessThan = false;
        if (col == "BankName")
        {
          // If this criterion is equal, move on to the next one
          std::string valA = a.getBankName();
          std::string valB = b.getBankName();
          // Move on to lesser criterion if equal
          if (valA == valB)
            continue;
          lessThan = (valA < valB);
        }
        else
        {
          // General double comparison
          double valA = a.getValueByColName(col);
          double valB = b.getValueByColName(col);
          // Move on to lesser criterion if equal
          if (valA == valB)
            continue;
          lessThan = (valA < valB);
        }
        // Flip the sign of comparison if descending.
        if (ascending)
          return lessThan;
        else
          return !lessThan;

      }
      // If you reach here, all criteria were ==; so not <, so return false
      return false;
    }
  };


  //---------------------------------------------------------------------------------------------
  /** Sort the peaks by one or more criteria
   *
   * @param criteria : a vector with a list of pairs: column name, bool;
   *        where bool = true for ascending, false for descending sort.
   *        The peaks are sorted by the first criterion first, then the 2nd if equal, etc.
   */
  void PeaksWorkspace::sort(std::vector< std::pair<std::string, bool> > & criteria)
  {
    PeakComparator comparator(criteria);
    std::stable_sort(peaks.begin(), peaks.end(), comparator);
  }

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  //---------------------------------------------------------------------------------------------
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  /** Destructor */
  PeaksWorkspace::~PeaksWorkspace()
  {
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//    ClearDeleteCalibrationData();
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  }

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  //---------------------------------------------------------------------------------------------
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  //---------------------------------------------------------------------------------------------
  /** Add a column (used by constructor). */
  bool PeaksWorkspace::addColumn(const std::string& type, const std::string& name)
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  {
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    UNUSED_ARG(type)
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    // Create the PeakColumn.
    columns.push_back( boost::shared_ptr<Mantid::DataObjects::PeakColumn>(new Mantid::DataObjects::PeakColumn( this->peaks, name) ) );
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    // Cache the names
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    columnNames.push_back(name);
    return true;
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  }

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  //---------------------------------------------------------------------------------------------
  /// @return the index of the column with the given name.
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  int PeaksWorkspace::getColumnIndex(const std::string& name) const
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  {
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    for (int i=0; i < int(columns.size()); i++)
      if (columns[i]->name() == name)
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        return i;
    throw std::invalid_argument("Column named " + name + " was not found in the PeaksWorkspace.");
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  }

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  //---------------------------------------------------------------------------------------------
  /// Gets the shared pointer to a column by index.
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  boost::shared_ptr<Mantid::API::Column> PeaksWorkspace::getColumn(int index)
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  {
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    if (index >= static_cast<int>(columns.size())) throw std::invalid_argument("PeaksWorkspace::getColumn() called with invalid index.");
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    return columns[index];
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  }

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  //---------------------------------------------------------------------------------------------
  /// Gets the shared pointer to a column by index.
  boost::shared_ptr<const Mantid::API::Column> PeaksWorkspace::getColumn(int index) const
  {
    if (index >= static_cast<int>(columns.size())) throw std::invalid_argument("PeaksWorkspace::getColumn() called with invalid index.");
    return columns[index];
  }
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  void PeaksWorkspace::saveNexus(::NeXus::File * file ) const
  {
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	int pNum = getNumberPeaks();

	// Column vectors for peaks table
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    std::vector<int> detectorID;
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    std::vector<double> H;
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	std::vector<double> K;
	std::vector<double> L;
	std::vector<double> intensity;
	std::vector<double> sigmaIntensity;
	std::vector<double> binCount;
	std::vector<double> initialEnergy;
	std::vector<double> finalEnergy;
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	std::vector<double> waveLength;
	std::vector<double> scattering;
	std::vector<double> dSpacing;
	std::vector<double> TOF;
    std::vector<int> runNumber;
	std::vector<double> goniometerMatrix;
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	// Populate column vectors from Peak Workspace
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	for (size_t i=0; i < peaks.size(); i++)
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	  {
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	    Peak p = peaks[i];
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        detectorID.push_back( p.getDetectorID() );  
        H.push_back( p.getH() );
		K.push_back( p.getK() );
		L.push_back( p.getL() );
		intensity.push_back( p.getIntensity() );
		sigmaIntensity.push_back( p.getSigmaIntensity() );
		binCount.push_back( p.getBinCount() );
		initialEnergy.push_back( p.getInitialEnergy() );
		finalEnergy.push_back( p.getFinalEnergy() );
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		waveLength.push_back( p.getWavelength() );
		scattering.push_back( p.getScattering() );
		dSpacing.push_back( p.getDSpacing() );
		TOF.push_back( p.getTOF() );
		runNumber.push_back( p.getRunNumber() );
		{
		   Matrix<double> gm = p.getGoniometerMatrix();
		   goniometerMatrix.push_back( gm[0][0]);
		   goniometerMatrix.push_back( gm[1][0]);
		   goniometerMatrix.push_back( gm[2][0]);
		   goniometerMatrix.push_back( gm[0][1]);
		   goniometerMatrix.push_back( gm[1][1]);
		   goniometerMatrix.push_back( gm[2][1]);
		   goniometerMatrix.push_back( gm[0][2]);
		   goniometerMatrix.push_back( gm[1][2]);
		   goniometerMatrix.push_back( gm[1][2]);
		}
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      // etc.
	  }
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	// Start Peaks Workspace in Nexus File
    file->makeGroup("peaks_workspace", "NXentry", true);  // For when peaksWorkspace can be loaded 
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    // Detectors column
	file->writeData("column_1", detectorID);
	file->openData("column_1");
	file->putAttr("name", "Dectector ID");
	file->putAttr("interpret_as","An integer");
	file->putAttr("units","Not known");
	file->closeData();

	// H column
    file->writeData("column_2", H);
	file->openData("column_2");
	file->putAttr("name", "H");
	file->putAttr("interpret_as","A double");
	file->putAttr("units","Not known");  // Units may need changing when known
	file->closeData();

	// K column
    file->writeData("column_3", K);
	file->openData("column_3");
	file->putAttr("name", "K");
	file->putAttr("interpret_as","A double");
	file->putAttr("units","Not known");  // Units may need changing when known
	file->closeData();

	// L column
    file->writeData("column_4", L);
	file->openData("column_4");
	file->putAttr("name", "L");
	file->putAttr("interpret_as","A double");
	file->putAttr("units","Not known");  // Units may need changing when known
	file->closeData();

	// Intensity column
	file->writeData("column_5", intensity);
	file->openData("column_5");
	file->putAttr("name", "Intensity");
	file->putAttr("interpret_as","A double");
	file->putAttr("units","Not known");  // Units may need changing when known
	file->closeData();

	// Sigma Intensity column
	file->writeData("column_6", sigmaIntensity);
	file->openData("column_6");
	file->putAttr("name", "Sigma Intensity");
	file->putAttr("interpret_as","A double");
	file->putAttr("units","Not known");  // Units may need changing when known
	file->closeData();

	// Bin Count column
	file->writeData("column_7", binCount);
	file->openData("column_7");
	file->putAttr("name", "Bin Count");
	file->putAttr("interpret_as","A double");
	file->putAttr("units","Not known");  // Units may need changing when known
	file->closeData();

    // Initial Energy column
	file->writeData("column_8", initialEnergy );
	file->openData("column_8");
	file->putAttr("name", "Initial Energy");
	file->putAttr("interpret_as","A double");
	file->putAttr("units","Not known");  // Units may need changing when known
	file->closeData();

    // Final Energy column
	file->writeData("column_9", finalEnergy );
	file->openData("column_9");
	file->putAttr("name", "Final Energy");
	file->putAttr("interpret_as","A double");
	file->putAttr("units","Not known");  // Units may need changing when known
	file->closeData();

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	// Wave Length Column
	file->writeData("column_10", waveLength );
	file->openData("column_10");
	file->putAttr("name", "Wave Length");
	file->putAttr("interpret_as","A double");
	file->putAttr("units","Not known");  // Units may need changing when known
	file->closeData();

	// Scattering Column
	file->writeData("column_11", scattering );
	file->openData("column_11");
	file->putAttr("name", "Scattering");
	file->putAttr("interpret_as","A double");
	file->putAttr("units","Not known");  // Units may need changing when known
	file->closeData();

	// D Spacing Column
	file->writeData("column_12", dSpacing );
	file->openData("column_12");
	file->putAttr("name", "D Spacing");
	file->putAttr("interpret_as","A double");
	file->putAttr("units","Not known");  // Units may need changing when known
	file->closeData();

	// TOF Column
	file->writeData("column_13", TOF );
	file->openData("column_13");
	file->putAttr("name", "TOF");
	file->putAttr("interpret_as","A double");
	file->putAttr("units","Not known");  // Units may need changing when known
	file->closeData();

	//Run Number column
	file->writeData("column_14", runNumber );
	file->openData("column_14");
	file->putAttr("name", "Run Number");
	file->putAttr("interpret_as","A integer");
	file->putAttr("units","Not known");  // Units may need changing when known
	file->closeData();

	// Goniometer Matrix Column
	std::vector<int> array_dims;
	array_dims.push_back(peaks.size());
    array_dims.push_back(9);
	file->writeData("column_15", goniometerMatrix, array_dims);
	file->openData("column_15");
	file->putAttr("name", "Goniometer Matrix");
	file->putAttr("interpret_as","A matrix of 3x3 doubles");
	file->putAttr("units","Not known");  // Units may need changing when known
	file->closeData();

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	file->closeGroup(); // end of peaks workpace

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  }
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}
}
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///\cond TEMPLATE

namespace Mantid
{
  namespace Kernel
  {

    template<> DLLExport
    Mantid::DataObjects::PeaksWorkspace_sptr IPropertyManager::getValue<Mantid::DataObjects::PeaksWorkspace_sptr>(const std::string &name) const
    {
      PropertyWithValue<Mantid::DataObjects::PeaksWorkspace_sptr>* prop =
        dynamic_cast<PropertyWithValue<Mantid::DataObjects::PeaksWorkspace_sptr>*>(getPointerToProperty(name));
      if (prop)
      {
        return *prop;
      }
      else
      {
        std::string message = "Attempt to assign property "+ name +" to incorrect type. Expected PeaksWorkspace.";
        throw std::runtime_error(message);
      }
    }

    template<> DLLExport
    Mantid::DataObjects::PeaksWorkspace_const_sptr IPropertyManager::getValue<Mantid::DataObjects::PeaksWorkspace_const_sptr>(const std::string &name) const
    {
      PropertyWithValue<Mantid::DataObjects::PeaksWorkspace_sptr>* prop =
        dynamic_cast<PropertyWithValue<Mantid::DataObjects::PeaksWorkspace_sptr>*>(getPointerToProperty(name));
      if (prop)
      {
        return prop->operator()();
      }
      else
      {
        std::string message = "Attempt to assign property "+ name +" to incorrect type. Expected const PeaksWorkspace.";
        throw std::runtime_error(message);
      }
    }

  } // namespace Kernel
} // namespace Mantid

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///\endcond TEMPLATE