LoadSpice2D.cpp

//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
#include "MantidDataHandling/LoadSpice2D.h"
#include "MantidAPI/FileProperty.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/ConfigService.h"
#include "MantidAPI/AlgorithmFactory.h"
#include "Poco/Path.h"
#include "Poco/StringTokenizer.h"
#include "Poco/DOM/DOMParser.h"
#include "Poco/DOM/Document.h"
#include "Poco/DOM/Element.h"
#include "Poco/DOM/NodeList.h"
#include "Poco/DOM/Node.h"
#include "Poco/DOM/Text.h"
#include "MantidAPI/SpectraDetectorMap.h"
#include <boost/shared_array.hpp>
#include <iostream>
//-----------------------------------------------------------------------

using Poco::XML::DOMParser;
using Poco::XML::Document;
using Poco::XML::Element;
using Poco::XML::NodeList;
using Poco::XML::Node;
using Poco::XML::Text;


namespace Mantid
{
  namespace DataHandling
  {
    // Parse string and convert to numeric type
    template <class T>
    bool from_string(T& t, const std::string& s, std::ios_base& (*f)(std::ios_base&))
    {
      std::istringstream iss(s);
      return !(iss >> f >> t).fail();
    }

    /**
     *  Convenience function to read in from an XML element
     *  @param t: variable to feed the data in
     *  @param pRootElem: element to read from
     *  @param element: name of the element to read
     *  @param fileName: file path
     */
    template <class T>
    bool from_element(T& t, Element* pRootElem,  const std::string& element, const std::string& fileName)
    {
      Element* sasEntryElem = pRootElem->getChildElement(element);
      if (!sasEntryElem) throw Kernel::Exception::NotFoundError(element + " element not found in Spice XML file", fileName);
      std::stringstream value_str(sasEntryElem->innerText());
      return !(value_str >> t).fail();
    }

    /**
     * Convenience function to store a detector value into a given spectrum.
     * Note that this type of data doesn't use TOD, so that we use a single dummy
     * bin in X. Each detector is defined as a spectrum of length 1.
     * @param ws: workspace
     * @param specID: ID of the spectrum to store the value in
     * @param value: value to store [count]
     * @param error: error on the value [count]
     * @param wavelength: wavelength value [Angstrom]
     * @param dwavelength: error on the wavelength [Angstrom]
     */
    void store_value(DataObjects::Workspace2D_sptr ws, int specID,
        double value, double error, double wavelength, double dwavelength)
    {
      MantidVec& X = ws->dataX(specID);
      MantidVec& Y = ws->dataY(specID);
      MantidVec& E = ws->dataE(specID);
      // The following is mostly to make Mantid happy by defining a histogram with
      // a single bin around the neutron wavelength
      X[0] = wavelength-dwavelength/2.0;
      X[1] = wavelength+dwavelength/2.0;
      Y[0] = value;
      E[0] = error;
      ws->getAxis(1)->spectraNo(specID) = specID;
    }


    // Register the algorithm into the AlgorithmFactory
    DECLARE_ALGORITHM(LoadSpice2D)

    /// Constructor
    LoadSpice2D::LoadSpice2D() {}

    /// Destructor
    LoadSpice2D::~LoadSpice2D() {}

    /// Overwrites Algorithm Init method.
    void LoadSpice2D::init()
    {
      declareProperty(new API::FileProperty("Filename", "", API::FileProperty::Load, ".xml"),
          "The name of the input xml file to load");
      declareProperty(new API::WorkspaceProperty<API::Workspace>("OutputWorkspace", "",
          Kernel::Direction::Output), "The name of the Output workspace");

      // Optionally, we can specify the wavelength and wavelength spread and overwrite
      // the value in the data file (used when the data file is not populated)
      Kernel::BoundedValidator<double> *mustBePositive = new Kernel::BoundedValidator<double>();
      mustBePositive->setLower(0.0);
      declareProperty("Wavelength", EMPTY_DBL(), mustBePositive,
          "Wavelength value to use when loading the data file (Angstrom).");
      declareProperty("WavelengthSpread", 0.1, mustBePositive->clone(),
        "Wavelength spread to use when loading the data file (default 0.0)" );

    }

    /// Overwrites Algorithm exec method
    void LoadSpice2D::exec()
    {
      std::string fileName = getPropertyValue("Filename");

      const double wavelength_input = getProperty("Wavelength");
      const double wavelength_spread_input = getProperty("WavelengthSpread");

      // Set up the DOM parser and parse xml file
      DOMParser pParser;
      Document* pDoc;
      try
      {
        pDoc = pParser.parse(fileName);
      } catch (...)
      {
        throw Kernel::Exception::FileError("Unable to parse File:", fileName);
      }
      // Get pointer to root element
      Element* pRootElem = pDoc->documentElement();
      if (!pRootElem->hasChildNodes())
      {
        throw Kernel::Exception::NotFoundError("No root element in Spice XML file", fileName);
      }
      Element* sasEntryElem = pRootElem->getChildElement("Header");
      throwException(sasEntryElem, "Header", fileName);

      // Read in scan title
      Element* element = sasEntryElem->getChildElement("Scan_Title");
      throwException(element, "Scan_Title", fileName);
      std::string wsTitle = element->innerText();

      // Read in instrument name
      element = sasEntryElem->getChildElement("Instrument");
      throwException(element, "Instrument", fileName);
      std::string instrument = element->innerText();

      // Read in the detector dimensions
      int numberXPixels = 0;
      from_element<int>(numberXPixels, sasEntryElem, "Number_of_X_Pixels", fileName);

      int numberYPixels = 0;
      from_element<int>(numberYPixels, sasEntryElem, "Number_of_Y_Pixels", fileName);

      // Read in wavelength and wavelength spread
      double wavelength = 0;
      double dwavelength = 0;
      if ( isEmpty(wavelength_input) ) {
        from_element<double>(wavelength, sasEntryElem, "wavelength", fileName);
        from_element<double>(dwavelength, sasEntryElem, "wavelength_spread", fileName);
      }
      else
      {
        wavelength = wavelength_input;
        dwavelength = wavelength_spread_input;
      }

      // Read in positions
      sasEntryElem = pRootElem->getChildElement("Motor_Positions");
      throwException(sasEntryElem, "Motor_Positions", fileName);

      // Read in sample-detector distance in mm
      double distance = 0;
      from_element<double>(distance, sasEntryElem, "sample_det_dist", fileName);
      distance *= 1000.0;

      // Read in counters
      sasEntryElem = pRootElem->getChildElement("Counters");
      throwException(sasEntryElem, "Counters", fileName);

      double countingTime = 0;
      from_element<double>(countingTime, sasEntryElem, "time", fileName);
      double monitorCounts = 0;
      from_element<double>(monitorCounts, sasEntryElem, "monitor", fileName);

      // Read in the data image
      Element* sasDataElem = pRootElem->getChildElement("Data");
      throwException(sasDataElem, "Data", fileName);

      // Read in the data buffer
      element = sasDataElem->getChildElement("Detector");
      throwException(element, "Detector", fileName);
      std::string data_str = element->innerText();

      // Store sample-detector distance
      declareProperty("SampleDetectorDistance", distance, Kernel::Direction::Output);

      // Create the output workspace

      // Number of bins: we use a single dummy TOF bin
      int nBins = 1;
      // Number of detectors: should be pulled from the geometry description. Use detector pixels for now.
      // The number of spectram also includes the monitor and the timer.
      int numSpectra = numberXPixels*numberYPixels + LoadSpice2D::nMonitors;

      DataObjects::Workspace2D_sptr ws = boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
          API::WorkspaceFactory::Instance().create("Workspace2D", numSpectra, nBins+1, nBins));
      ws->setTitle(wsTitle);
      ws->getAxis(0)->unit() = Kernel::UnitFactory::Instance().create("Wavelength");
      ws->setYUnit("");
      API::Workspace_sptr workspace = boost::static_pointer_cast<API::Workspace>(ws);
      setProperty("OutputWorkspace", workspace);

      // Parse out each pixel. Pixels can be separated by white space, a tab, or an end-of-line character
      Poco::StringTokenizer pixels(data_str, " \n\t", Poco::StringTokenizer::TOK_TRIM | Poco::StringTokenizer::TOK_IGNORE_EMPTY);
      Poco::StringTokenizer::Iterator pixel = pixels.begin();

      // Check that we don't keep within the size of the workspace
      int pixelcount = pixels.count();
      if( pixelcount != numberXPixels*numberYPixels )
      {
        throw Kernel::Exception::FileError("Inconsistent data set: "
            "There were more data pixels found than declared in the Spice XML meta-data.", fileName);
      }
      if( numSpectra == 0 )
      {
        throw Kernel::Exception::FileError("Empty data set: the data file has no pixel data.", fileName);
      }

      // Go through all detectors/channels
      int ipixel = 0;

      // Store monitor count
      store_value(ws, ipixel++, monitorCounts, monitorCounts>0 ? sqrt(monitorCounts) : 0.0,
          wavelength, dwavelength);

      // Store counting time
      store_value(ws, ipixel++, countingTime, 0.0, wavelength, dwavelength);

      // Store detector pixels
      while (pixel != pixels.end())
      {
        //int ix = ipixel%npixelsx;
        //int iy = (int)ipixel/npixelsx;

        // Get the count value and assign it to the right bin
        double count = 0.0;
        from_string<double>(count, *pixel, std::dec);

        // Data uncertainties, computed according to the HFIR/IGOR reduction code
        // The following is what I would suggest instead...
        // error = count > 0 ? sqrt((double)count) : 0.0;
        double error = sqrt( 0.5 + fabs( count - 0.5 ));

        store_value(ws, ipixel, count, error, wavelength, dwavelength);

        // Set the spectrum number
        ws->getAxis(1)->spectraNo(ipixel) = ipixel;

        ++pixel;
        ipixel++;
      }

      // run load instrument
      runLoadInstrument(instrument, ws);
      runLoadMappingTable(ws, numberXPixels, numberYPixels);

      // Set the sample-detector distance
      boost::shared_ptr<Mantid::API::IInstrument> i = ws->getInstrument();
      boost::shared_ptr<Mantid::Geometry::IComponent> sample = i->getSample();

      Geometry::ParameterMap &pmap = ws->instrumentParameters();
      pmap.add("double", i.get(), "sample-detector-distance", distance);

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

      // Finding the name of the detector object.
      // The detector bank is the parent of the first non-monitor detector.
      Geometry::IDetector_const_sptr det_pixel = ws->getDetector(LoadSpice2D::nMonitors);
      boost::shared_ptr<const Mantid::Geometry::IComponent> detector_bank = det_pixel->getParent();
      std::string detID = detector_bank->getName();
      try
      {
        mover->setProperty<API::MatrixWorkspace_sptr> ("Workspace", ws);
        mover->setProperty("ComponentName", detID);
        mover->setProperty("Z", distance/1000.0);
        mover->execute();
      } catch (std::invalid_argument& e)
      {
        g_log.error("Invalid argument to MoveInstrumentComponent sub-algorithm");
        g_log.error(e.what());
      } catch (std::runtime_error& e)
      {
        g_log.error("Unable to successfully run MoveInstrumentComponent sub-algorithm");
        g_log.error(e.what());
      }

    }

    /** Run the sub-algorithm LoadInstrument (as for LoadRaw)
     * @param inst_name The name written in the Nexus file
     * @param localWorkspace The workspace to insert the instrument into
     */
    void LoadSpice2D::runLoadInstrument(const std::string & inst_name,
        DataObjects::Workspace2D_sptr localWorkspace)
    {
      // Determine the search directory for XML instrument definition files (IDFs)
      std::string directoryName = Kernel::ConfigService::Instance().getString(
          "instrumentDefinition.directory");
      if (directoryName.empty())
      {
        // This is the assumed deployment directory for IDFs, where we need to be relative to the
        // directory of the executable, not the current working directory.
        directoryName = Poco::Path(Mantid::Kernel::ConfigService::Instance().getBaseDir()).resolve(
            "../Instrument").toString();
      }

      // For Nexus Mantid processed, Instrument XML file name is read from nexus
      std::string instrumentID = inst_name;
      // force ID to upper case
      std::transform(instrumentID.begin(), instrumentID.end(), instrumentID.begin(), toupper);
      std::string fullPathIDF = directoryName + "/" + instrumentID + "_Definition.xml";

      API::IAlgorithm_sptr loadInst = createSubAlgorithm("LoadInstrument");

      // Now execute the sub-algorithm. Catch and log any error, but don't stop.
      try
      {
        loadInst->setPropertyValue("Filename", fullPathIDF);
        loadInst->setProperty<API::MatrixWorkspace_sptr> ("Workspace", localWorkspace);
        loadInst->execute();
      } catch (std::invalid_argument&)
      {
        g_log.information("Invalid argument to LoadInstrument sub-algorithm");
      } catch (std::runtime_error&)
      {
        g_log.information("Unable to successfully run LoadInstrument sub-algorithm");
      }
    }

    /**
     * Populate spectra mapping to detector IDs
     *
     * TODO: Get the detector size information from the workspace directly
     *
     * @param localWorkspace: Workspace2D object
     * @param nxbins: number of bins in X
     * @param nybins: number of bins in Y
     */
    void LoadSpice2D::runLoadMappingTable(DataObjects::Workspace2D_sptr localWorkspace, int nxbins, int nybins)
    {
      // Get the number of monitor channels
      int nMonitors = 0;
      boost::shared_ptr<API::Instrument> instrument = localWorkspace->getBaseInstrument();
      std::vector<int> monitors = instrument->getMonitors();
      nMonitors = monitors.size();

      // Number of monitors should be consistent with data file format
      if( nMonitors != LoadSpice2D::nMonitors ) {
        std::stringstream error;
        error << "Geometry error for " << instrument->getName() <<
            ": Spice data format defines " << LoadSpice2D::nMonitors << " monitors, " << nMonitors << " were/was found";
        throw std::runtime_error(error.str());
      }

      int ndet = nxbins*nybins + nMonitors;
      boost::shared_array<int> udet(new int[ndet]);
      boost::shared_array<int> spec(new int[ndet]);

      // Generate mapping of detector/channel IDs to spectrum ID

      // Detector/channel counter
      int icount = 0;

      // Monitor: IDs start at 1 and increment by 1
      for(int i=0; i<nMonitors; i++)
      {
        spec[icount] = icount;
        udet[icount] = icount+1;
        icount++;
      }

      // Detector pixels
      for(int ix=0; ix<nxbins; ix++)
      {
        for(int iy=0; iy<nybins; iy++)
        {
          spec[icount] = icount;
          udet[icount] = 1000000 + iy*1000 + ix;
          icount++;
        }
      }

      // Populate the Spectra Map with parameters
      localWorkspace->mutableSpectraMap().populate(spec.get(), udet.get(), ndet);
    }


    /* This method throws not found error if a element is not found in the xml file
     * @param elem pointer to  element
     * @param name  element name
     * @param fileName xml file name
     */
    void LoadSpice2D::throwException(Poco::XML::Element* elem, const std::string & name,
        const std::string& fileName)
    {
      if (!elem)
      {
        throw Kernel::Exception::NotFoundError(name + " element not found in Spice XML file", fileName);
      }
    }
}
}