LoadIDFFromNexus.cpp

//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
#include "MantidDataHandling/LoadIDFFromNexus.h"
#include "MantidKernel/ConfigService.h"
#include "MantidAPI/FileProperty.h"
#include <Poco/Path.h>
#include <Poco/File.h>
#include <Poco/DOM/Document.h>
#include <Poco/DOM/DOMParser.h>
#include <Poco/DOM/Element.h>
#include <Poco/DOM/NodeList.h>
#include <Poco/DOM/NodeIterator.h>

using Poco::XML::DOMParser;
using Poco::XML::Document;
using Poco::XML::Element;
using Poco::XML::NodeList;
using Poco::XML::NodeIterator;

namespace Mantid {
namespace DataHandling {

DECLARE_ALGORITHM(LoadIDFFromNexus)

using namespace Kernel;
using namespace API;
using Geometry::Instrument;

/// Empty default constructor
LoadIDFFromNexus::LoadIDFFromNexus() {}

/// Initialisation method.
void LoadIDFFromNexus::init() {
  // When used as a Child Algorithm the workspace name is not used - hence the
  // "Anonymous" to satisfy the validator
  declareProperty(
      new WorkspaceProperty<MatrixWorkspace>("Workspace", "Anonymous",
                                             Direction::InOut),
      "The name of the workspace in which to attach the imported instrument");

  std::vector<std::string> exts;
  exts.push_back(".nxs");
  exts.push_back(".nxs.h5");
  declareProperty(
      new FileProperty("Filename", "", FileProperty::Load, exts),
      "The name (including its full or relative path) of the Nexus file to "
      "attempt to load the instrument from.");

  declareProperty("InstrumentParentPath", std::string(""),
                  "Path name within the Nexus tree of the folder containing "
                  "the instrument folder. "
                  "For example it is 'raw_data_1' for an ISIS raw Nexus file "
                  "and 'mantid_workspace_1' for a processed nexus file. "
                  "Only a one level path is curently supported",
                  Direction::Input);
}

/** Executes the algorithm. Reading in the file and creating and populating
 *  the output workspace
 *
 *  @throw FileError Thrown if unable to parse XML file
 */
void LoadIDFFromNexus::exec() {
  // Retrieve the filename from the properties
  const std::string filename = getPropertyValue("Filename");

  // Get the input workspace
  const MatrixWorkspace_sptr localWorkspace = getProperty("Workspace");

  // Get the instrument path
  std::string instrumentParentPath = getPropertyValue("InstrumentParentPath");

  // Get the instrument group in the Nexus file
  ::NeXus::File nxfile(filename);
  // Assume one level in instrument path
  nxfile.openPath(instrumentParentPath);

  // Take instrument info from nexus file.
  localWorkspace->loadInstrumentInfoNexus(filename, &nxfile );

  // Look for parameter correction file
  std::string parameterCorrectionFile = getParameterCorrectionFile( localWorkspace->getInstrument()->getName() );
  g_log.debug() << "Parameter correction file: " << parameterCorrectionFile << "\n";

  // Read parameter correction file, if found
  std::string correctionParameterFile = "";
  bool append = false;
  if( parameterCorrectionFile != "") {
    // Read parameter correction file 
    // to find out which parameter file to use 
    // and whether it is appended to default parameters.
    readParameterCorrectionFile( parameterCorrectionFile, localWorkspace->getAvailableWorkspaceStartDate(), correctionParameterFile, append );
  }


  // Load default parameters if either there is no correction parameter file or it is to be appended.
  if( correctionParameterFile == "" || append ) {
    LoadParameters(  &nxfile, localWorkspace );
  }

  // Load parameters from correction parameter file, if it exists
  if( correctionParameterFile != "") {
      Poco::Path corrFilePath(parameterCorrectionFile);
      g_log.debug() << "Correction file path: " << corrFilePath.toString() << "\n";
      Poco::Path corrDirPath = corrFilePath.parent();
      g_log.debug() << "Correction directory path: " << corrDirPath.toString() << "\n";
      Poco::Path corrParamFile( corrDirPath, correctionParameterFile );
      g_log.debug() << "Using readParameterCorrectionFile: " << corrParamFile.toString() << " " << append << "\n";
      bool ok = loadParameterFile( corrParamFile.toString(), localWorkspace );
      if(!ok) {
        g_log.error() << "Unable to load parameter file " << corrParamFile.toString() << " specified in " << corrFilePath.toString() << ".\n";
      }
  }

  return;
}

  /*  Gets the full pathname of the parameter correction file, if it exists
   * @param instName :: short name of instrument as it appears in IDF filename etc.
   * @returns  full path name of correction file if found else ""
  */
  std::string LoadIDFFromNexus::getParameterCorrectionFile( const std::string& instName ) {

    std::vector<std::string> directoryNames =
      ConfigService::Instance().getInstrumentDirectories();
    for (auto instDirs_itr = directoryNames.begin();
      instDirs_itr != directoryNames.end(); ++instDirs_itr) {
        // This will iterate around the directories from user ->etc ->install, and
        // find the first appropriate file
        Poco::Path iPath( *instDirs_itr,"embedded_instrument_corrections"); // Go to correction file subfolder
        // First see if the directory exists
        Poco::File ipDir(iPath);
        if( ipDir.exists() && ipDir.isDirectory() ) {
          iPath.append(instName + "_Parameter_Corrections.xml"); // Append file name to pathname
            Poco::File ipFile(iPath);
            if( ipFile.exists() && ipFile.isFile())
            {
              return ipFile.path(); // Return first found
            }
        } // Directory
    } // Loop
    return ""; // No file found
  }


  /* Reads the parameter correction file and if a correction is needed output the parameterfile needed 
  *  and whether it is to be appended.
  * @param correction_file :: path nsame of correction file as returned by getParameterCorrectionFile()
  * @param date :: IS8601 date string applicable: Must be full timestamp (timezone optional)
  * @param parameter_file :: output parameter file to use or "" if none
  * @param append :: output whether the parameters from parameter_file should be appended.
  *
  *  @throw FileError Thrown if unable to parse XML file
  */
void LoadIDFFromNexus::readParameterCorrectionFile( const std::string& correction_file, const std::string& date, 
                                                   std::string& parameter_file, bool& append ) {

   // Set output arguments to default
  parameter_file = "";
  append = false;

  // Check the date.
  if( date == ""){
    g_log.notice() << "No date is supplied for parameter correction file " << correction_file << ". Correction file is ignored.\n";
    return;
  }

   // Get contents of correction file                                                    
  const std::string xmlText = Kernel::Strings::loadFile(correction_file);

  // Set up the DOM parser and parse xml file
  DOMParser pParser;
  Document* pDoc;
  try {
    pDoc = pParser.parseString(xmlText);
  } catch (Poco::Exception &exc) {
    throw Kernel::Exception::FileError(
        exc.displayText() + ". Unable to parse parameter correction file:", correction_file);
  } catch (...) {
    throw Kernel::Exception::FileError("Unable to parse parameter correction file:", correction_file);
  }
  // Get pointer to root element
  Element* pRootElem = pDoc->documentElement();
  if (!pRootElem->hasChildNodes()) {
    g_log.error("Parameter correction file: " + correction_file + "contains no XML root element.");
    throw Kernel::Exception::InstrumentDefinitionError(
        "No root element in XML parameter correction file", correction_file);
  }

  // Convert date to Mantid object
  g_log.notice() << "Date for correction file " << date << "\n";
  DateAndTime externalDate( date );

  // Examine the XML structure obtained by parsing
  Poco::AutoPtr<NodeList> correctionNodeList = pRootElem->getElementsByTagName("correction");
  for( unsigned long i=0; i < correctionNodeList->length(); ++i ){
    // For each correction element
    Element* corr = (Element *)correctionNodeList->item(i);
    DateAndTime start(corr->getAttribute("valid-from"));
    DateAndTime end(corr->getAttribute("valid-to"));
    if ( start <= externalDate && externalDate <= end ){
      parameter_file = corr->getAttribute("file");
      append = ( corr->getAttribute("append") == "true");
      break;  
    }
  }
  
}


/** Loads the parameters from the Nexus file if possible, else from a parameter file
 *  into the specified workspace
 * @param nxfile :: open NeXus file
 * @param localWorkspace :: workspace into which loading occurs
 *
 *  @throw FileError Thrown if unable to parse XML file
 */
void LoadIDFFromNexus::LoadParameters( ::NeXus::File *nxfile, const MatrixWorkspace_sptr localWorkspace ) {

  std::string parameterString;

  // First attempt to load parameters from nexus file.                                    
  nxfile->openGroup("instrument", "NXinstrument");
  localWorkspace->loadInstrumentParametersNexus( nxfile, parameterString );
  nxfile->closeGroup();

  // loadInstrumentParametersNexus does not populate any instrument params
  // so we do it here.
  localWorkspace->populateInstrumentParameters();

  if (parameterString.empty()) {
    // No parameters have been found in Nexus file, so we look for them in a parameter file.
    std::vector<std::string> directoryNames =
        ConfigService::Instance().getInstrumentDirectories();
    const std::string instrumentName =
        localWorkspace->getInstrument()->getName();
    for (auto instDirs_itr = directoryNames.begin();
         instDirs_itr != directoryNames.end(); ++instDirs_itr) {
      // This will iterate around the directories from user ->etc ->install, and
      // find the first appropriate file
      std::string directoryName = *instDirs_itr;
      const std::string paramFile =
          directoryName + instrumentName + "_Parameters.xml";

      // Attempt to load specified file, if successful, use file and stop search.
      if(loadParameterFile( paramFile, localWorkspace )) break; 

    }
  } else { // We do have parameters from the Nexus file
    g_log.notice()
        << "Found Instrument parameter map entry in Nexus file, which is loaded.\n"
        << std::endl;
    // process parameterString into parameters in workspace
    localWorkspace->readParameterMap(parameterString);
  }

}

// Private function to load parameter file specified by a full path name into given workspace, returning success.
bool LoadIDFFromNexus::loadParameterFile (const std::string& fullPathName, const MatrixWorkspace_sptr localWorkspace ) {
 
      try {
        // load and also populate instrument parameters from this 'fallback'
        // parameter file
        Algorithm_sptr loadParamAlg = createChildAlgorithm("LoadParameterFile");
        loadParamAlg->setProperty("Filename", fullPathName);
        loadParamAlg->setProperty("Workspace", localWorkspace);
        loadParamAlg->execute();
        g_log.notice() << "Instrument parameter file: " << fullPathName
                       << " has been loaded.\n" << std::endl;
        return true; // Success 
      } catch (std::runtime_error &) {
        g_log.debug() << "Instrument parameter file: " << fullPathName
                      << " not found or un-parsable.\n";
        return false; // Failure
      }
}


} // namespace DataHandling
} // namespace Mantid