MantidUI.cpp

#include "PythonSystemHeader.h"
#include "MantidUI.h"
#include "MantidMatrix.h"
#include "MantidDock.h"
#include "ImportWorkspaceDlg.h"
#include "AlgorithmMonitor.h"
#include "MantidSampleLogDialog.h"
#include "MantidSampleMaterialDialog.h"
#include "AlgorithmHistoryWindow.h"
#include "MantidMatrixCurve.h"
#include "MantidMDCurve.h"
#include "MantidMDCurveDialog.h"
#include "MantidQtMantidWidgets/FitPropertyBrowser.h"
#include "MantidTable.h"
#include "../../MantidQt/MantidWidgets/ui_SequentialFitDialog.h"
#include "../Spectrogram.h"
#include "../pixmaps.h"
#include "../ScriptingWindow.h"
#include "../Folder.h"
#include "../TiledWindow.h"

#include "MantidKernel/Property.h"
#include "MantidKernel/ConfigService.h"
#include "MantidKernel/DateAndTime.h"
#include "MantidKernel/LogFilter.h"
#include "MantidKernel/DateAndTime.h"
#include "MantidKernel/UnitConversion.h"
#include "InstrumentWidget/InstrumentWindow.h"
#include "MantidKernel/TimeSeriesProperty.h"

#include "MantidQtAPI/AlgorithmInputHistory.h"
#include "MantidQtAPI/InterfaceManager.h"
#include "MantidQtAPI/PlotAxis.h"
#include "MantidQtAPI/VatesViewerInterface.h"

#include "MantidKernel/EnvironmentHistory.h"
#include "MantidKernel/ConfigService.h"
#include "MantidKernel/FacilityInfo.h"

#include "MantidAPI/CompositeFunction.h"
#include "MantidAPI/ITableWorkspace.h"
#include "MantidAPI/IMDHistoWorkspace.h"


#include <QMessageBox>
#include <QTextEdit>
#include <QListWidget>
#include <QMdiArea>
#include <QMenuBar>
#include <QApplication>
#include <QToolBar>
#include <QMenu>
#include <QInputDialog>

#include <qwt_plot_curve.h>
#include <algorithm>
#include <time.h>

#ifdef _WIN32
#include <windows.h>
#endif

#include <algorithm>
#include <locale>
#include <set>
#include <fstream>
#include <iostream>
#include <sstream>

#include <boost/tokenizer.hpp>

#include <Poco/ActiveResult.h>

#include "MantidAPI/IMDWorkspace.h"
#include "MantidQtSliceViewer/SliceViewerWindow.h"
#include "MantidQtFactory/WidgetFactory.h"
#include "MantidAPI/MemoryManager.h"

#include "MantidQtSpectrumViewer/SpectrumView.h"
#include <typeinfo>

using namespace std;

using namespace Mantid::API;
using Mantid::Kernel::DateAndTime;
using MantidQt::SliceViewer::SliceViewerWindow;

namespace MantidException = Mantid::Kernel::Exception;

namespace
{
  /// The number of detectors to show within a group before eliding
  size_t DET_TABLE_NDETS_GROUP = 10;

  // Initialize logger
  Mantid::Kernel::Logger g_log("MantidUI");
}


MantidUI::MantidUI(ApplicationWindow *aw):
  m_finishedLoadDAEObserver(*this, &MantidUI::handleLoadDAEFinishedNotification),
  m_addObserver(*this,&MantidUI::handleAddWorkspace),
  m_replaceObserver(*this,&MantidUI::handleReplaceWorkspace),
  m_deleteObserver(*this,&MantidUI::handleDeleteWorkspace),
  m_clearADSObserver(*this,&MantidUI::handleClearADS),
  m_renameObserver(*this,&MantidUI::handleRenameWorkspace),
  m_groupworkspacesObserver(*this,&MantidUI::handleGroupWorkspaces),
  m_ungroupworkspaceObserver(*this,&MantidUI::handleUnGroupWorkspace),
  m_workspaceGroupUpdateObserver(*this,&MantidUI::handleWorkspaceGroupUpdate),
  m_configServiceObserver(*this,&MantidUI::handleConfigServiceUpdate),
  m_appWindow(aw),
  m_lastShownInstrumentWin(NULL), m_lastShownSliceViewWin(NULL), m_lastShownSpectrumViewerWin(NULL), 
  m_lastShownColorFillWin(NULL), m_lastShown1DPlotWin(NULL), 
  m_vatesSubWindow(NULL)//, m_spectrumViewWindow(NULL)
{

  // To be able to use them in queued signals they need to be registered
  static bool registered_addtional_types = false;
  if( !registered_addtional_types )
  {
    registered_addtional_types = true;
    qRegisterMetaType<Mantid::API::Workspace_sptr>();
    qRegisterMetaType<Mantid::API::MatrixWorkspace_sptr>();
    qRegisterMetaType<Mantid::API::MatrixWorkspace_const_sptr>();
    //Register std::string as well as we use it alot
    qRegisterMetaType<std::string>();
  }

  m_exploreMantid = new MantidDockWidget(this,aw);
  m_exploreAlgorithms = new AlgorithmDockWidget(this,aw);

  actionCopyRowToTable = new QAction(this);
  actionCopyRowToTable->setIcon(QIcon(getQPixmap("table_xpm")));
  connect(actionCopyRowToTable, SIGNAL(activated()), this, SLOT(copyRowToTable()));

  actionCopyRowToGraph = new QAction(this);
  actionCopyRowToGraph->setIcon(QIcon(getQPixmap("graph_xpm")));
  connect(actionCopyRowToGraph, SIGNAL(activated()), this, SLOT(copyRowToGraph()));

  actionCopyRowToGraphErr = new QAction(this);
  actionCopyRowToGraphErr->setIcon(QIcon(getQPixmap("graph_xpm")));
  connect(actionCopyRowToGraphErr, SIGNAL(activated()), this, SLOT(copyRowToGraphErr()));

  actionWaterfallPlot = new QAction(QIcon(":/waterfall_plot.png"), tr("Plot spectra as waterfall"), this);
  connect(actionWaterfallPlot, SIGNAL(activated()), this, SLOT(copyRowsToWaterfall()));

  actionCopyDetectorsToTable = new QAction(tr("View detectors table"), this);
  actionCopyDetectorsToTable->setIcon(QIcon(getQPixmap("table_xpm")));
  connect(actionCopyDetectorsToTable, SIGNAL(activated()), this, SLOT(copyDetectorsToTable()));

  actionCopyValues = new QAction(tr("Copy"), this);
  actionCopyValues->setIcon(QIcon(getQPixmap("copy_xpm")));
  connect(actionCopyValues, SIGNAL(activated()), this, SLOT(copyValues()));

  actionCopyColumnToTable = new QAction(this);
  actionCopyColumnToTable->setIcon(QIcon(getQPixmap("table_xpm")));
  connect(actionCopyColumnToTable, SIGNAL(activated()), this, SLOT(copyColumnToTable()));

  actionCopyColumnToGraph = new QAction(this);
  actionCopyColumnToGraph->setIcon(QIcon(getQPixmap("graph_xpm")));
  connect(actionCopyColumnToGraph, SIGNAL(activated()), this, SLOT(copyColumnToGraph()));

  actionCopyColumnToGraphErr = new QAction(this);
  actionCopyColumnToGraphErr->setIcon(QIcon(getQPixmap("graph_xpm")));
  connect(actionCopyColumnToGraphErr, SIGNAL(activated()), this, SLOT(copyColumnToGraphErr()));

  connect(this,SIGNAL(needToCreateLoadDAEMantidMatrix(const QString&)),this,SLOT(createLoadDAEMantidMatrix(const QString&)));
  connect(this,SIGNAL(needToShowCritical(const QString&)),this,SLOT(showCritical(const QString&)));

  m_algMonitor = new AlgorithmMonitor(this);
  connect(m_algMonitor,SIGNAL(algorithmStarted(void*)),m_exploreAlgorithms,SLOT(algorithmStarted(void*)), Qt::QueuedConnection);
  connect(m_algMonitor,SIGNAL(algorithmFinished(void*)),m_exploreAlgorithms,SLOT(algorithmFinished(void*)), Qt::QueuedConnection);
  connect(m_algMonitor,SIGNAL(needUpdateProgress(void*,double, const QString&, double, int)),
    m_exploreAlgorithms,SLOT(updateProgress(void*,double, const QString&, double, int)), Qt::QueuedConnection);
  m_algMonitor->start();

  mantidMenu = new QMenu(m_appWindow);
  mantidMenu->setObjectName("mantidMenu");
  // for activating the keyboard shortcut for Clear All Memory even if no clciking on Mantid Menu
  // Ticket #672
  //connect(mantidMenu, SIGNAL(aboutToShow()), this, SLOT(mantidMenuAboutToShow()));
  mantidMenuAboutToShow();

  QShortcut* sc = new QShortcut(QKeySequence(QKeySequence::Delete), m_appWindow);
  connect(sc, SIGNAL(activated()), this, SLOT(deletePressEvent()));

  menuMantidMatrix = new QMenu(m_appWindow);
  connect(menuMantidMatrix, SIGNAL(aboutToShow()), this, SLOT(menuMantidMatrixAboutToShow()));

  init();
}

// Should it be moved to the constructor?
void MantidUI::init()
{
  AnalysisDataServiceImpl &dataStore = AnalysisDataService::Instance();
  dataStore.notificationCenter.addObserver(m_addObserver);
  dataStore.notificationCenter.addObserver(m_replaceObserver);
  dataStore.notificationCenter.addObserver(m_deleteObserver);
  dataStore.notificationCenter.addObserver(m_clearADSObserver);
  dataStore.notificationCenter.addObserver(m_renameObserver);
  dataStore.notificationCenter.addObserver(m_groupworkspacesObserver);
  dataStore.notificationCenter.addObserver(m_ungroupworkspaceObserver);
  dataStore.notificationCenter.addObserver(m_workspaceGroupUpdateObserver);
  Mantid::Kernel::ConfigService::Instance().addObserver(m_configServiceObserver);

  m_exploreAlgorithms->update();

  try
  {
    m_defaultFitFunction = new MantidQt::MantidWidgets::FitPropertyBrowser(m_appWindow, this);
    m_defaultFitFunction->init();
    // this make the progress bar work with Fit algorithm running form the fit browser
    connect(m_defaultFitFunction,SIGNAL(executeFit(QString,QHash<QString,QString>,Mantid::API::AlgorithmObserver*)),
      this,SLOT(showAlgorithmDialog(QString,QHash<QString,QString>,Mantid::API::AlgorithmObserver*)));
    m_defaultFitFunction->hide();
    m_appWindow->addDockWidget( Qt::LeftDockWidgetArea, m_defaultFitFunction );

    m_fitFunction = m_defaultFitFunction;
  }
  catch(...)
  {
    m_defaultFitFunction = NULL;
    m_fitFunction = NULL;
    showCritical("The curve fitting plugin is missing");
  }

}

/// Slot: Receives a new X range from a FitPropertyBrowser and re-emits it.
void MantidUI::x_range_from_picker(double xmin, double xmax)
{
  emit x_range_update(xmin, xmax);
}

/// Updates the algorithms tree as this may have changed
void MantidUI::updateAlgorithms()
{
  m_exploreAlgorithms->update();
}

/// Show / hide the AlgorithmDockWidget
void MantidUI::showAlgWidget(bool on)
{
  if (on)
  {
    m_exploreAlgorithms->show();
  }
  else
  {
    m_exploreAlgorithms->hide();
  }
}

void MantidUI::addMenuItems(QMenu *menu)
{
  actionToggleMantid = m_exploreMantid->toggleViewAction();
  actionToggleMantid->setIcon(getQPixmap("mantid_matrix_xpm"));
  actionToggleMantid->setShortcut( tr("Ctrl+Shift+M") );
  menu->addAction(actionToggleMantid);

  actionToggleAlgorithms = m_exploreAlgorithms->toggleViewAction();
  actionToggleAlgorithms->setShortcut( tr("Ctrl+Shift+A") );
  menu->addAction(actionToggleAlgorithms);

  if (m_fitFunction)
  {
    actionToggleFitFunction = m_fitFunction->toggleViewAction();
    menu->addAction(actionToggleFitFunction);
  }

}

// Show / hide the FitPropertyBrowser
void MantidUI::showFitPropertyBrowser(bool on)
{
  if (!m_fitFunction) return;
  if (on)
  {
    m_fitFunction->show();
  }
  else
  {
    m_fitFunction->hide();
  }
}

/**
* Be careful where this is called, if it is a called too late in the Qt shutdown the application
* crashes
*/
void MantidUI::shutdown()
{
  g_log.notice("MantidPlot is shutting down...");

  // First we need to cancel any running algorithms otherwise bad things can happen if they call
  // the logging framework after it's been shutdown. The cancel calls within cancelAll are not
  // blocking, hence the loop to make sure they're all done before moving on. (N.B. Tried copying
  // the wait/exit/wait business from the AlgorithmMonitor dtor, but that gave occasional crashes.)
  if ( m_algMonitor )
  {
    m_algMonitor->cancelAll();
    while ( m_algMonitor->count() > 0 )
    {
      Poco::Thread::sleep(100);
    }
  }

  Mantid::API::FrameworkManager::Instance().clear();
}

MantidUI::~MantidUI()
{
  delete m_algMonitor;

  Mantid::Kernel::ConfigService::Instance().removeObserver(m_configServiceObserver);
  Mantid::API::AnalysisDataService::Instance().notificationCenter.removeObserver(m_groupworkspacesObserver);
  Mantid::API::AnalysisDataService::Instance().notificationCenter.removeObserver(m_ungroupworkspaceObserver);
  Mantid::API::AnalysisDataService::Instance().notificationCenter.removeObserver(m_workspaceGroupUpdateObserver);
  Mantid::API::AnalysisDataService::Instance().notificationCenter.removeObserver(m_addObserver);
  Mantid::API::AnalysisDataService::Instance().notificationCenter.removeObserver(m_replaceObserver);
  Mantid::API::AnalysisDataService::Instance().notificationCenter.removeObserver(m_deleteObserver);
  Mantid::API::AnalysisDataService::Instance().notificationCenter.removeObserver(m_clearADSObserver);

  delete m_fitFunction;
}

void MantidUI::saveSettings() const
{
  // Save algorithm dialog input
  MantidQt::API::AlgorithmInputHistory::Instance().save();
}

QStringList MantidUI::getWorkspaceNames()
{
  QStringList sl;
  std::set<std::string> sv = Mantid::API::AnalysisDataService::Instance().getObjectNames();
  for (std::set<std::string>::const_iterator it = sv.begin(); it != sv.end(); ++it)
    sl<<QString::fromStdString(*it);
  return sl;
}

QStringList MantidUI::getAlgorithmNames()
{
  QStringList sl;
  std::vector<std::string> sv;
  sv = Mantid::API::AlgorithmFactory::Instance().getKeys();
  for(size_t i=0;i<sv.size();i++)
    sl<<QString::fromStdString(sv[i]);
  return sl;
}

/**
*  Returns the number of algorithms currently executing
*/
int MantidUI::runningAlgCount() const
{
  return m_algMonitor->count();
}

/**
* Ticket #678
*/
void MantidUI::saveNexusWorkspace()
{
  executeSaveNexus();
}

/**
* DeleteWorkspace
@param workspaceName :: Name of the workspace to delete
*/
void MantidUI::deleteWorkspace(const QString& workspaceName)
{
  auto alg = createAlgorithm("DeleteWorkspace");
  alg->setLogging(false);
  alg->setPropertyValue("Workspace",workspaceName.toStdString());
  executeAlgorithmAsync(alg);
}

/**
getSelectedWorkspaceName
*/
QString MantidUI::getSelectedWorkspaceName()
{
  QString str = m_exploreMantid->getSelectedWorkspaceName();
  if ( str.isEmpty() )
  {
    //Check if a mantid matrix is selected
    MantidMatrix *m = qobject_cast<MantidMatrix*>(appWindow()->activeWindow());
    if( !m ) return "";

    str = m->workspaceName();
  }
  return str;
}

Mantid::API::Workspace_const_sptr MantidUI::getSelectedWorkspace()
{
  return m_exploreMantid->getSelectedWorkspace();
}

Mantid::API::Workspace_const_sptr MantidUI::getWorkspace(const QString& workspaceName)
{
  if (AnalysisDataService::Instance().doesExist(workspaceName.toStdString()))
  {
    return AnalysisDataService::Instance().retrieve(workspaceName.toStdString());
  }

  Workspace_sptr empty;

  return empty;//??
}

/**   Extension to ApplicationWindow::menuAboutToShow() to deal with Mantid.
*/
bool MantidUI::menuAboutToShow(MdiSubWindow *w)
{

  if (w && w->isA("MantidMatrix"))
  {
    appWindow()->myMenuBar()->insertItem(tr("3D &Plot"), appWindow()->plot3DMenu);
    appWindow()->actionCopySelection->setEnabled(true);
    appWindow()->actionPasteSelection->setEnabled(false);
    appWindow()->actionClearSelection->setEnabled(false);

    appWindow()->myMenuBar()->insertItem(tr("&Workspace"),menuMantidMatrix);
    return true;
  }

  return false;
}

Graph3D *MantidUI::plot3DMatrix(int style)
{	
  MdiSubWindow *w = appWindow()->activeWindow();
  if (w->isA("MantidMatrix"))
  {
    return static_cast<MantidMatrix*>(w)->plotGraph3D(style);
  }

  return 0;
}

MultiLayer* MantidUI::plotSpectrogram(Graph::CurveType type)
{
  MantidMatrix *m = dynamic_cast<MantidMatrix*>(appWindow()->activeWindow());
  if (m)
  {
    return drawSingleColorFillPlot(QString::fromStdString(m->getWorkspaceName()), type);
  }
  return 0;
}

/**  Import a MatrixWorkspace into a MantidMatrix.
@param wsName :: Workspace name
@param lower :: An optional lower boundary
@param upper :: An optional upper boundary
@param showDlg :: If true show a dialog box to set some import parameters
@param makeVisible :: If true show the created MantidMatrix, hide otherwise.
@return A pointer to the new MantidMatrix.
*/
MantidMatrix* MantidUI::importMatrixWorkspace(const QString& wsName, int lower, int upper, bool showDlg, bool makeVisible)
{
  MatrixWorkspace_sptr ws;
  if (AnalysisDataService::Instance().doesExist(wsName.toStdString()))
  {
    ws = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(wsName.toStdString());
  }

  if (!ws.get()) return 0;

  MantidMatrix* w = 0;
  if (showDlg)
  {
    ImportWorkspaceDlg dlg(appWindow(), ws->getNumberHistograms());
    if (dlg.exec() == QDialog::Accepted)
    {
      int start = dlg.getLowerLimit();
      int end = dlg.getUpperLimit();

      w = new MantidMatrix(ws, appWindow(), "Mantid",wsName, start, end );
      if (dlg.isFiltered())
        w->setRange(0,dlg.getMaxValue());
    }
  }
  else
  {
    w = new MantidMatrix(ws, appWindow(), "Mantid",wsName, lower, upper);
  }
  if ( !w ) return 0;

  appWindow()->addMdiSubWindow(w,makeVisible);
  return w;
}

/**  Import a Workspace into MantidPlot.
@param wsName :: Workspace name
@param showDlg :: If true show a dialog box to set some import parameters
@param makeVisible :: If true show the created widget, hide otherwise.
*/
void MantidUI::importWorkspace(const QString& wsName, bool showDlg, bool makeVisible)
{
  MantidMatrix* mm = importMatrixWorkspace(wsName,-1, -1, showDlg,makeVisible);
  QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
  if (!mm)
  {
    importTableWorkspace(wsName,showDlg,makeVisible);
  }
  QApplication::restoreOverrideCursor();
}

/**  Import the selected workspace, if any. Displays the import dialog.
*/
void MantidUI::importWorkspace()
{
  QString wsName = getSelectedWorkspaceName();
  importWorkspace(wsName,true,true);
}

/**  Import the selected table workspace transposed.
*/
void MantidUI::importTransposed()
{
  QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
  QString wsName = getSelectedWorkspaceName();
  ITableWorkspace_sptr ws;
  if (AnalysisDataService::Instance().doesExist(wsName.toStdString()))
  {
    ws = AnalysisDataService::Instance().retrieveWS<ITableWorkspace>(wsName.toStdString());
    importTableWorkspace(wsName,true,true,true);
  }
  QApplication::restoreOverrideCursor();
}


/**  Create a TableWorkspace of box data from the MDEventWorkspace
*/
void MantidUI::importBoxDataTable()
{
  std::cout << "MantidUI::importBoxDataTable()" << std::endl;
  QString wsName = getSelectedWorkspaceName();
  try
  {
    // Get the MD event table
    IMDEventWorkspace_sptr ws = boost::dynamic_pointer_cast<IMDEventWorkspace>(
      AnalysisDataService::Instance().retrieve( wsName.toStdString()) );
    if (!ws) return;
    ITableWorkspace_sptr tabWs = ws->makeBoxTable(0,0);
    if (!tabWs) return;
    std::string tableName = wsName.toStdString() + std::string("_boxdata");
    AnalysisDataService::Instance().addOrReplace(tableName, tabWs);
    // Now show that table
    importWorkspace(QString::fromStdString(tableName), true, true);
  }
  catch (...)
  {
  }
}

/** Plots a Curve showing intensities for a MDWorkspace.
* But only if the workspace meets certain criteria, such as
* having only one non-integrated dimension. Should exit gracefully otherwise.
*/
void MantidUI::showMDPlot()
{
  QString wsName = getSelectedWorkspaceName();

  // Create a dialog to ask for options
  MantidMDCurveDialog dlg(appWindow(), wsName);
  if ( dlg.exec() == QDialog::Rejected )
    return;
  // Extract the settings from the dialog opened earlier
  bool showErrors = dlg.showErrorBars();
  LinePlotOptions * opts = dlg.getLineOptionsWidget();
  QStringList all;
  all << wsName;
  plotMDList(all, opts->getPlotAxis(), opts->getNormalization(), showErrors);
}

/**
 * Plots a curve showing intensities for MDWorkspaces
 * @param wsNames : Names of the workspaces to plot
 * @param plotAxis : Axis number to plot
 * @param normalization: Normalization option to use
 * @param showErrors: True if errors are to be show
 * @param plotWindow :: Window to use for plotting. If NULL a new one will be created
 * @param clearWindow :: Whether to clean the plotWindow before plotting.Ignored if plotWindow == NULL
 * @return NULL if failure. Otherwise, if plotWindow == NULL - created window, if not NULL - plotWindow
 */
MultiLayer* MantidUI::plotMDList(const QStringList& wsNames, const int plotAxis, 
  const Mantid::API::MDNormalization normalization, const bool showErrors, MultiLayer* plotWindow, 
  bool clearWindow)
{
  QApplication::setOverrideCursor(QCursor(Qt::WaitCursor)); 

  auto firstName = wsNames.at(0);

  bool isGraphNew = false;
  MultiLayer* ml = appWindow()->prepareMultiLayer(isGraphNew, plotWindow, firstName, clearWindow);

  Graph *g = ml->activeGraph();
  try
  {
    for (int i = 0; i < wsNames.size(); ++i)
    {
      // Create the curve with defaults
      auto wsName = wsNames.at(i);
      MantidMDCurve* curve = new MantidMDCurve(wsName, g, showErrors);
      MantidQwtIMDWorkspaceData * data = curve->mantidData();

      // Apply the settings
      data->setPreviewMode(false);
      data->setPlotAxisChoice(plotAxis);
      data->setNormalization(normalization);

      // Using information from the first graph
      if( i == 0 && isGraphNew )
      {
        g->setXAxisTitle(data->getXAxisLabel());
        g->setYAxisTitle(data->getYAxisLabel());
        g->setAutoScale();
      }
    }

  }
  catch (std::invalid_argument &e)
  {
    g_log.warning() << e.what() << std::endl;
  }
  catch (std::runtime_error &e)
  {
    g_log.warning() << e.what() << std::endl;
  }
  catch (...)
  {}

  if(!isGraphNew)
    // Replot graph is we've added curves to existing one
    g->replot();

  // Check if window does not contain any curves and should be closed
  ml->maybeNeedToClose();

  QApplication::restoreOverrideCursor();

  return ml;
}

/*
Generates a table workspace from a md workspace and pulls up
a grid to display the results.
*/
void MantidUI::showListData()
{
  QString wsName = getSelectedWorkspaceName();
  QString tableWsName = wsName + "_data_list_table";

  Mantid::API::IAlgorithm_sptr queryWorkspace = this->createAlgorithm("QueryMDWorkspace");
  queryWorkspace->initialize();
  queryWorkspace->setPropertyValue("InputWorkspace", wsName.toStdString());
  std::string sTableWorkspaceName=tableWsName.toStdString();
  queryWorkspace->setPropertyValue("OutputWorkspace", sTableWorkspaceName);
  queryWorkspace->setProperty("LimitRows", false);
  queryWorkspace->execute();

  importWorkspace(tableWsName);
}

void MantidUI::showVatesSimpleInterface()
{
  QString wsName = getSelectedWorkspaceName();
  try
  {
    IMDEventWorkspace_sptr mdews = boost::dynamic_pointer_cast<IMDEventWorkspace>(
      AnalysisDataService::Instance().retrieve( wsName.toStdString()) );

    IPeaksWorkspace_sptr pws = boost::dynamic_pointer_cast<IPeaksWorkspace>(
      AnalysisDataService::Instance().retrieve(wsName.toStdString()));

    IMDHistoWorkspace_sptr mdhist = boost::dynamic_pointer_cast<IMDHistoWorkspace>(
      AnalysisDataService::Instance().retrieve( wsName.toStdString()) );

    if (!mdews && !pws && !mdhist)
    {
      return;
    }
    // Set the type of workspace, the GUI needs it
    int wsType = MantidQt::API::VatesViewerInterface::MDEW;
    if (pws)
    {
      wsType = MantidQt::API::VatesViewerInterface::PEAKS;
    }
    if (mdhist)
    {
      wsType = MantidQt::API::VatesViewerInterface::MDHW;
    }

    if (m_vatesSubWindow)
    {
      QWidget *vwidget = m_vatesSubWindow->widget();
      vwidget->show();
      qobject_cast<MantidQt::API::VatesViewerInterface *>(vwidget)->renderWorkspace(wsName, wsType);
      return;
    }
    else
    {
      m_vatesSubWindow = new QMdiSubWindow;
      m_vatesSubWindow->setAttribute(Qt::WA_DeleteOnClose, false);
      QIcon icon; icon.addFile(QString::fromUtf8(":/VatesSimpleGuiViewWidgets/icons/pvIcon.png"), QSize(), QIcon::Normal, QIcon::Off);
      m_vatesSubWindow->setWindowIcon(icon);
      connect(m_appWindow, SIGNAL(shutting_down()), m_vatesSubWindow, SLOT(close()));

      MantidQt::API::InterfaceManager interfaceManager;
      MantidQt::API::VatesViewerInterface *vsui = interfaceManager.createVatesSimpleGui();
      if (vsui)
      {
        connect(m_appWindow, SIGNAL(shutting_down()),
          vsui, SLOT(shutdown()));
        connect(vsui, SIGNAL(requestClose()), m_vatesSubWindow, SLOT(close()));
        vsui->setParent(m_vatesSubWindow);
        m_vatesSubWindow->setWindowTitle("Vates Simple Interface");
        vsui->setupPluginMode();
        //m_appWindow->setGeometry(m_vatesSubWindow, vsui);
        m_vatesSubWindow->setWidget(vsui);
        m_vatesSubWindow->widget()->show();
        vsui->renderWorkspace(wsName, wsType);
      }
      else
      {
        delete m_vatesSubWindow;
        m_vatesSubWindow = NULL;
        return;
      }
    }
  }
  catch (std::runtime_error &e)
  {
    throw std::runtime_error(e);
  }
  catch (...)
  {
  }
}

void MantidUI::showSpectrumViewer()
{
  QString wsName = getSelectedWorkspaceName();
  try
  {
    MatrixWorkspace_sptr wksp = boost::dynamic_pointer_cast<MatrixWorkspace>(
      AnalysisDataService::Instance().retrieve( wsName.toStdString()) );
    if ( wksp )
    {
      MantidQt::SpectrumView::SpectrumView* viewer;
      try
      {
        viewer = new MantidQt::SpectrumView::SpectrumView(m_appWindow);
      }
      catch (std::runtime_error& e)
      {
        m_lastShownSpectrumViewerWin = NULL;
        g_log.error() << "Could not create spectrum viewer: " << e.what() << "\n";
        throw std::runtime_error(e);
      }
      viewer->setAttribute(Qt::WA_DeleteOnClose, false);
      viewer->resize( 1050, 800 );
      connect(m_appWindow, SIGNAL(shutting_down()), viewer, SLOT(close()));

      if (workspacesDockPlot1To1())
      {
        // only one at any given time
        if (m_lastShownSpectrumViewerWin)
        {
          m_lastShownSpectrumViewerWin->close();
          QPoint p = m_lastShownSpectrumViewerWin->pos();
          delete m_lastShownSpectrumViewerWin;
          viewer->move(p);
        }

      }
      m_lastShownSpectrumViewerWin = viewer;

      viewer->show();
      viewer->renderWorkspace(wksp);
    }
    else
    {
      g_log.information() << "Only event or matrix workspaces are currently supported.\n"
        << "Please convert to one of these before using the ImageView.\n";
    }
  }
  catch (std::runtime_error &e)
  {
    g_log.error() << e.what() << "\n";
    throw std::runtime_error(e);
  }
  catch (...)
  {
    g_log.error() << "Image View: Exception getting workspace\n";
  }

}


/** Create a window with a SliceViewer widget to show
* the selected workspace
*/
void MantidUI::showSliceViewer()
{
  // Retrieve the MDWorkspace
  QString wsName = getSelectedWorkspaceName();
  IMDWorkspace_sptr mdws = boost::dynamic_pointer_cast<IMDWorkspace>(
    AnalysisDataService::Instance().retrieve( wsName.toStdString()) );
  MatrixWorkspace_sptr mw = boost::dynamic_pointer_cast<MatrixWorkspace>(mdws);
  if (mdws)
  {
    // Create the slice viewer window
    SliceViewerWindow * w;
    try
    {
      w = MantidQt::Factory::WidgetFactory::Instance()->createSliceViewerWindow(wsName, "");
    }
    catch (std::runtime_error& e)
    {
      m_lastShownSliceViewWin = NULL;
      g_log.error() << "Could not create slice viewer: " << e.what() << "\n";
      throw std::runtime_error(e);
    }

    // Special options for viewing MatrixWorkspaces
    if (mw)
    {
      w->getSlicer()->setTransparentZeros(false);
    }

    // Connect the MantidPlot close() event with the the window's close().
    QObject::connect(appWindow(), SIGNAL(destroyed()), w, SLOT(close()));

    if (workspacesDockPlot1To1())
    {
      // only one at any given time
      if (m_lastShownSliceViewWin)
      {
        m_lastShownSliceViewWin->close();
        QPoint p = m_lastShownSliceViewWin->pos();
        // the factory keeps a list of all opened slice viewers
        MantidQt::Factory::WidgetFactory::Instance()->closeSliceViewerWindow(m_lastShownSliceViewWin);
        delete m_lastShownSliceViewWin;
        w->move(p);
      }
    }
    m_lastShownSliceViewWin = w;

    // Pop up the window
    w->show();
    // And add it
    //appWindow()->d_workspace->addSubWindow(w);
  }

}

/** #539: For adding Workspace History display to MantidPlot
Show Algorithm History Details in a window .
*/
void MantidUI::showAlgorithmHistory()
{
  QString wsName=getSelectedWorkspaceName();
  Mantid::API::Workspace_const_sptr wsptr=getWorkspace(wsName);
  if(NULL != wsptr) 
  {
    // If the workspace has any AlgorithHistory ...
    if(!wsptr->getHistory().empty())
    {
      // ... create and display the window.
      AlgorithmHistoryWindow *palgHist = new AlgorithmHistoryWindow(m_appWindow,wsptr);
      if(NULL != palgHist)
      {
        palgHist->show();
      }
    }
  }
  else
  {
    QMessageBox::information(appWindow(),"Mantid","Invalid WorkSpace");
    return;
  }
}

/**  Create a new Table and fill it with the data from a Tableworkspace
@param wsName :: Workspace name
@param showDlg :: If true show a dialog box to set some import parameters
@param makeVisible :: If true show the created Table, hide otherwise.
@param transpose :: Transpose the table
@return A pointer to the new Table.
*/
Table* MantidUI::importTableWorkspace(const QString& wsName, bool, bool makeVisible, bool transpose)
{
  ITableWorkspace_sptr ws;
  if (AnalysisDataService::Instance().doesExist(wsName.toStdString()))
  {
    ws = AnalysisDataService::Instance().retrieveWS<ITableWorkspace>(wsName.toStdString());
  }

  if (!ws.get()) return 0;

  if (ws->rowCount() == 0 || ws->columnCount() == 0)
  {
    showCritical("Cannot create an empty table");
    return 0;
  }

  Table* t = new MantidTable(appWindow()->scriptingEnv(), ws, wsName, appWindow(), transpose);
  if (makeVisible) t->showNormal();
  else t->showMinimized();
  return t;
}

void MantidUI::showContextMenu(QMenu& cm, MdiSubWindow* w)
{
  if (w->isA("MantidMatrix"))
  {
    MantidMatrix * mm = dynamic_cast<MantidMatrix*>(w);

    bool areSpectraSelected = mm->setSelectedRows();
    bool areColumnsSelected = mm->setSelectedColumns();
    cm.addAction(actionCopyValues);
    if (areSpectraSelected) cm.addAction(actionCopyRowToTable);
    if (areColumnsSelected) cm.addAction(actionCopyColumnToTable);
    cm.addSeparator();
    cm.addAction(actionCopyDetectorsToTable);
    cm.addSeparator();

    if (areSpectraSelected && mm->numCols() > 1)
    {
      // Enable the appropriate options
      cm.addAction(actionCopyRowToGraph);
      cm.addAction(actionCopyRowToGraphErr);
      if (mm->getSelectedRows().size() > 1)
      {
        cm.addAction(actionWaterfallPlot);
      }
    }
    if (areColumnsSelected && mm->numRows() > 1)
    {
      cm.addAction(actionCopyColumnToGraph);
      cm.addAction(actionCopyColumnToGraphErr);
    }

    // Set the option texts to the correct plurality
    if (mm->getSelectedRows().size() > 1)
    {
      actionCopyRowToTable->setText("Copy spectra to table");
      actionCopyRowToGraph->setText("Plot spectra (values only)");
      actionCopyRowToGraphErr->setText("Plot spectra (values + errors)");
    }
    else
    {
      actionCopyRowToTable->setText("Copy spectrum to table");
      actionCopyRowToGraph->setText("Plot spectrum (values only)");
      actionCopyRowToGraphErr->setText("Plot spectrum (values + errors)");
    }
    if (mm->getSelectedColumns().size() > 1)
    {
      actionCopyColumnToTable->setText("Copy bins to table");
      actionCopyColumnToGraph->setText("Plot bins (values only)");
      actionCopyColumnToGraphErr->setText("Plot bins (values + errors)");
    }
    else
    {
      actionCopyColumnToTable->setText("Copy bin to table");
      actionCopyColumnToGraph->setText("Plot bin (values only)");
      actionCopyColumnToGraphErr->setText("Plot bin (values + errors)");
    }

  }
}

void MantidUI::copyRowToTable()
{
  MantidMatrix* m = dynamic_cast<MantidMatrix*>(appWindow()->activeWindow());
  if (!m || !m->isA("MantidMatrix")) return;
  Table* t = createTableFromSelectedRows(m,true,true);
  t->showNormal();
}

void MantidUI::copyColumnToTable()
{
  MantidMatrix* m = dynamic_cast<MantidMatrix*>(appWindow()->activeWindow());
  if (!m || !m->isA("MantidMatrix")) return;
  Table* t = createTableFromSelectedColumns(m,true);
  t->showNormal();
}

void MantidUI::copyRowToGraph()
{
  MantidMatrix* m = dynamic_cast<MantidMatrix*>(appWindow()->activeWindow());
  if (!m || !m->isA("MantidMatrix")) return;
  plotSelectedRows(m,MantidQt::DistributionDefault,false);

}

void MantidUI::copyColumnToGraph()
{
  MantidMatrix* m = dynamic_cast<MantidMatrix*>(appWindow()->activeWindow());
  if (!m || !m->isA("MantidMatrix")) return;
  plotSelectedColumns(m,false);
}

void MantidUI::copyColumnToGraphErr()
{
  MantidMatrix* m = dynamic_cast<MantidMatrix*>(appWindow()->activeWindow());
  if (!m || !m->isA("MantidMatrix")) return;
  plotSelectedColumns(m,true);
}

void MantidUI::copyRowToGraphErr()
{
  MantidMatrix* m = dynamic_cast<MantidMatrix*>(appWindow()->activeWindow());
  if (!m || !m->isA("MantidMatrix")) return;
  plotSelectedRows(m,MantidQt::DistributionDefault,true);

}

void MantidUI::copyRowsToWaterfall()
{
  const MantidMatrix* const m = dynamic_cast<MantidMatrix*>(appWindow()->activeWindow());
  if (!m || !m->isA("MantidMatrix")) return;
  MultiLayer* ml = plotSelectedRows(m, MantidQt::DistributionDefault, false);
  if (ml) convertToWaterfall(ml);
}

void MantidUI::plotWholeAsWaterfall()
{
  const MantidMatrix* const m = dynamic_cast<MantidMatrix*>(appWindow()->activeWindow());
  if (!m || !m->isA("MantidMatrix")) return;
  MultiLayer* ml = plotSpectraRange(m->workspaceName(),0,m->numRows()-1,
                                    MantidQt::DistributionDefault, false);
  if (ml) convertToWaterfall(ml);
}

void MantidUI::convertToWaterfall(MultiLayer* ml)
{
  ml->hide();
  ml->activeGraph()->setWaterfallOffset(10,20);
  ml->setWaterfallLayout();
  // Next two lines replace the legend so that it works on reversing the curve order
  ml->activeGraph()->removeLegend();
  ml->activeGraph()->newLegend();
  ml->show();
}

void MantidUI::copyDetectorsToTable()
{
  MantidMatrix* m = dynamic_cast<MantidMatrix*>(appWindow()->activeWindow());
  if (!m || !m->isA("MantidMatrix")) return;
  createTableDetectors(m);
}

void MantidUI::copyValues()
{
  MantidMatrix* m = dynamic_cast<MantidMatrix*>(appWindow()->activeWindow());
  if (!m || !m->isA("MantidMatrix")) return;
  m->copySelection();
}


Table* MantidUI::createTableDetectors(MantidMatrix *m)
{
  std::vector<int> indices(m->numRows(), 0);
  for(int i = 0; i < m->numRows();i++)
  {
    indices[i] = m->workspaceIndex(i);
  }
  return createDetectorTable(m->workspaceName(), indices);
}

/**
* Create the relevant detector table for the given workspace
* @param wsName :: The name of the workspace
* @param indices :: Limit the table to these workspace indices (MatrixWorkspace only)
* @param include_data :: If true then first value from the each spectrum is displayed (MatrixWorkspace only)
*/
Table* MantidUI::createDetectorTable(const QString & wsName, const std::vector<int>& indices, bool include_data)
{
  if( AnalysisDataService::Instance().doesExist(wsName.toStdString()) )
  {
    auto ws = AnalysisDataService::Instance().retrieve(wsName.toStdString());
    // Standard MatrixWorkspace
    auto matrix = boost::dynamic_pointer_cast<MatrixWorkspace>(ws);
    if(matrix) 
    {
      return createDetectorTable(wsName, matrix, indices, include_data);
    }
    auto peaks = boost::dynamic_pointer_cast<IPeaksWorkspace>(ws);
    if(peaks) 
    {
      return createDetectorTable(wsName, peaks);
    }
  }
  return NULL;
}	

/**
* Create the instrument detector table from a MatrixWorkspace
* @param wsName :: The name of the workspace
* @param ws :: A pointer to a MatrixWorkspace
* @param indices :: Limit the table to these workspace indices
* @param include_data :: If true then first value from the each spectrum is displayed
*/
Table* MantidUI::createDetectorTable(const QString & wsName, const Mantid::API::MatrixWorkspace_sptr & ws,
                                     const std::vector<int>& indices, bool include_data)
{
  using namespace Mantid::Geometry;

  //check if efixed value is available
  bool calcQ(true);
  try
  {
    auto detector = ws->getDetector(0);
    ws->getEFixed(detector);
  } catch(std::runtime_error&)
  {
    calcQ = false;
  }

  // Prepare column names. Types will be determined from QVariant
  QStringList colNames;
  colNames << "Index" << "Spectrum No" << "Detector ID(s)";
  if( include_data )
  {
    colNames << "Data Value" << "Data Error";
  }

  colNames << "R" << "Theta";
  if(calcQ)
  {
    colNames << "Q";
  }
  colNames << "Phi" << "Monitor";

  const int ncols = static_cast<int>(colNames.size());
  const int nrows = indices.empty()? static_cast <int>(ws->getNumberHistograms()) : static_cast<int>(indices.size());
  Table* t = new Table(appWindow()->scriptingEnv(), nrows, ncols, "", appWindow(), 0);
  appWindow()->initTable(t, appWindow()->generateUniqueName(wsName + "-Detectors-"));
  // Set the column names
  for( int col = 0; col < ncols; ++col )
  {
    t->setColName(col, colNames[col]);
    t->setColPlotDesignation(col, Table::None);
  }
  t->setHeaderColType();

  // Cache some frequently used values
  IComponent_const_sptr sample = ws->getInstrument()->getSample();
  bool signedThetaParamRetrieved(false), showSignedTwoTheta(false); //If true,  signedVersion of the two theta value should be displayed
  QVector<QList<QVariant> > tableColValues;
  tableColValues.resize(nrows);
  PARALLEL_FOR1( ws )
  for( int row = 0; row < nrows; ++row )
  {
    // Note PARALLEL_START_INTERUPT_REGION & friends apparently not needed (like in algorithms)
    // as there's an extensive try...catch below. If it was need, using those macros would
    // require data members and methods that are available in algorithm classed but not here,
    // including m_cancel, m_parallelException, interrrupt_point().
    QList<QVariant>& colValues = tableColValues[row];
    size_t wsIndex = indices.empty() ? static_cast<size_t>(row) : indices[row];
    colValues << QVariant(static_cast<double>(wsIndex));
    const double dataY0(ws->readY(wsIndex)[0]), dataE0(ws->readE(wsIndex)[0]);
    try
    {
      ISpectrum *spectrum = ws->getSpectrum(wsIndex);
      Mantid::specid_t specNo = spectrum->getSpectrumNo();
      QString detIds("");
      const auto & ids  = spectrum->getDetectorIDs();
      size_t ndets = ids.size();
      auto iter = ids.begin();
      auto itEnd = ids.end();
      if(ndets > DET_TABLE_NDETS_GROUP)
      {
        detIds = QString("%1,%2...(%3 more)...%4,%5");
        //post-fix increments and returns last value
        // NOTE: Doing this detIds.arg(*iter++).arg(*iter++).arg(ndets-4) seems to result
        // in an undefined order in which the iterator is dereference and incremented leading
        // to the first two items being backward on some systems
        const Mantid::detid_t first(*iter++), second(*iter++);
        detIds = detIds.arg(first).arg(second).arg(ndets-4); // First two + n extra
        auto revIter = ids.rbegin(); // Set iterators are unidirectional ... so no operator-()
        const Mantid::detid_t last(*revIter++), lastm1(*revIter++);
        detIds = detIds.arg(lastm1).arg(last);
      }
      else
      {
        for(; iter != itEnd; ++iter)
        {
          detIds += QString::number(*iter) + ",";
        }
        detIds.chop(1); //Drop last comma
      }

      // Geometry
      IDetector_const_sptr det = ws->getDetector(wsIndex);
      if(!signedThetaParamRetrieved)
      {
        const std::vector<std::string>& parameters = det->getStringParameter("show-signed-theta", true); //recursive
        showSignedTwoTheta = (!parameters.empty() && find(parameters.begin(), parameters.end(), "Always") != parameters.end());
        signedThetaParamRetrieved = true;
      }
      // We want the position of the detector relative to the sample
      Mantid::Kernel::V3D pos = det->getPos() - sample->getPos();
      double R(0.0), theta(0.0), phi(0.0);
      pos.getSpherical(R,theta,phi);
      // Need to get R, theta through these methods to be correct for grouped detectors
      R = det->getDistance(*sample);
      theta = showSignedTwoTheta ? ws->detectorSignedTwoTheta(det) : ws->detectorTwoTheta(det);
      theta *= 180.0/M_PI; //To degrees
      QString isMonitor = det->isMonitor() ? "yes" : "no";

      colValues << QVariant(specNo) << QVariant(detIds);
      // Y/E
      if(include_data)
      {
        colValues << QVariant(dataY0) << QVariant(dataE0); // data
      }
      colValues << QVariant(R) << QVariant(theta);

      if(calcQ)
      {

        try
        {
          // Get unsigned theta and efixed value
          double efixed = ws->getEFixed(det);
          double usignTheta = ws->detectorTwoTheta(det)/2.0;

          double q = Mantid::Kernel::UnitConversion::run(usignTheta, efixed);
          colValues << QVariant(q);
        }
        catch (std::runtime_error&)
        {
          colValues << QVariant("No Efixed");
        }
      }

      colValues << QVariant(phi) // rtp
                << QVariant(isMonitor);         // monitor
    }
    catch(...)
    {
      // spectrumNo=-1, detID=0
      colValues << QVariant(-1) << QVariant("0");
      // Y/E
      if(include_data)
      {
        colValues << QVariant(dataY0) << QVariant(dataE0); // data
      }
      colValues << QVariant("0") << QVariant("0") //rt
                << QVariant("0") // efixed
                << QVariant("0") // rtp
                << QVariant("n/a"); // monitor
    }// End catch for no spectrum
  }

  // This modifies widgets, so it needs to run in the Qt GUI thread: no openmp here
  for( int row = 0; row < nrows; ++row ) {
    const QList<QVariant>& colValues = tableColValues[row];
    for(int col = 0; col < ncols; ++col)
    {
      const QVariant& colValue = colValues[col];
      if(QMetaType::QString == colValue.userType()) // Avoid a compiler warning with type() about comparing different enums...
      {
        t->setText(row, col, colValue.toString());
      }
      else
      {
        t->setCell(row, col, colValue.toDouble());
      }
    }
  }
  t->showNormal();

  return t;
}

/**
* Creates a table showing the detectors contributing to the peaks within a PeaksWorkspace
* @param wsName :: The name of the workspace
* @param ws :: A pointer to an IPeaksWorkspace object
*/
Table* MantidUI::createDetectorTable(const QString & wsName, const Mantid::API::IPeaksWorkspace_sptr & ws)
{
  // Import the peaks table too for reference
  bool dialog(false), visible(true);
  importTableWorkspace(wsName,dialog,visible);

  auto idtable = ws->createDetectorTable();
  bool transpose = false;
  QString tableName = wsName + "-Detectors";
  Table* t = new MantidTable(appWindow()->scriptingEnv(), idtable, tableName, appWindow(), transpose);
  if(!t) return NULL;
  t->showNormal();
  return t;
}

/**
 * Triggered by a delete key press, and attempts to delete a workspace if it passes the focus checks 
 */
void MantidUI::deletePressEvent()
{
  m_exploreMantid->deleteWorkspaces();
}

/**
 * Check if drop event can be accepted
 */
bool MantidUI::canAcceptDrop(QDragEnterEvent *e)
{
  QString name = e->mimeData()->objectName();
  if ( name == "MantidWorkspace" || e->mimeData()->hasUrls() || name == "TiledWindow" )
  {
    return true;
  }
  return false;
}

bool MantidUI::drop(QDropEvent* e)
{
  QString name = e->mimeData()->objectName();
  if (name == "MantidWorkspace")
  {
    QString text = e->mimeData()->text();
    int endIndex = 0;
    QStringList wsNames;
    while (text.indexOf("[\"",endIndex) > -1)
    {
      int startIndex = text.indexOf("[\"",endIndex) + 2;
      endIndex = text.indexOf("\"]",startIndex);
      wsNames.append(text.mid(startIndex,endIndex-startIndex));
    }

    foreach (const auto& wsName, wsNames)
    {
      importWorkspace(wsName,false);
    }
    return true;
  }
  else if (e->mimeData()->hasUrls())
  {
    QStringList pyFiles = extractPyFiles(e->mimeData()->urls());
    if (pyFiles.size() > 0)
    {
      try
      {
        m_appWindow->openScriptWindow(pyFiles);
      }
      catch (std::runtime_error& error)
      {
        g_log.error()<<"Failed to Load the python files. The reason for failure is: "<< error.what()<<std::endl;
      }      
      catch (std::logic_error& error)
      {
        g_log.error()<<"Failed to Load the python files. The reason for failure is: "<< error.what()<<std::endl;
      }
    }
    else
    {
      //pass to Loading of mantid workspaces
      m_exploreMantid->dropEvent(e);
    }
    return true;
  }
  else if (name == "TiledWindow" )
  {
    MdiSubWindow *w = m_appWindow->currentFolder()->window( e->mimeData()->text() );
    if ( !w ) return false;
    TiledWindow *tw = dynamic_cast<TiledWindow*>( w );
    if ( !tw ) return false;
    tw->removeSelectionToDefaultWindowType();

    return true;
  }

  return false;
}

///extracts the files from a mimedata object that have a .py extension
QStringList MantidUI::extractPyFiles(const QList<QUrl>& urlList) const
{
  QStringList filenames;
  for (int i = 0; i < urlList.size(); ++i) 
  {
    QString fName = urlList[i].toLocalFile();
    if (fName.size()>0)
    {
      QFileInfo fi(fName);
      
      if (fi.suffix().upper()=="PY")
      {
        filenames.append(fName);
      }
    }
  }
  return filenames;
}

/**
executes Save Nexus
saveNexus Input Dialog is a generic dialog.Below code is added to remove
the workspaces except the selected workspace from the InputWorkspace combo

*/
void MantidUI::executeSaveNexus()
{
  QString wsName = getSelectedWorkspaceName();
  QHash<QString,QString> presets;
  if (!wsName.isEmpty())
  {
    presets["InputWorkspace"] = wsName;
  }
  showAlgorithmDialog("SaveNexus", presets);
}

//-----------------------------------------------------------------------------
/** Open an algorithm dialog to execute the named algorithm.
*
* @param algName :: name of the algorithm
* @param version :: version number, -1 for latest
* @return true if sucessful.
*/
void MantidUI::showAlgorithmDialog(const QString & algName, int version)
{
  Mantid::API::IAlgorithm_sptr alg = this->createAlgorithm(algName, version);
  if( !alg ) return;
  MantidQt::API::AlgorithmDialog* dlg = createAlgorithmDialog(alg);

  if (algName == "Load")
  {
    // when loading files, we'll need to update the list of recent files
    // hook up MantidUI::fileDialogAccept() to the LoadDialog dialog accepted() signal
    connect(dlg, SIGNAL(accepted()), this, SLOT(loadFileDialogAccept()));
  }

  dlg->show();
  dlg->raise();
  dlg->activateWindow();
}

/**
* Execute an algorithm. Show the algorithm dialog before executing. The property widgets will be preset
*   with values in paramList.
* @param algName :: The algorithm name
* @param paramList :: A list of algorithm properties to be passed to Algorithm::setProperties
* @param obs :: A pointer to an instance of AlgorithmObserver which will be attached to the finish notification
*/
void MantidUI::showAlgorithmDialog(QString algName, QHash<QString,QString> paramList, Mantid::API::AlgorithmObserver *obs)
{
  //Get latest version of the algorithm
  Mantid::API::IAlgorithm_sptr alg = this->createAlgorithm(algName, -1);
  if( !alg ) return;

  for(QHash<QString,QString>::Iterator it = paramList.begin(); it != paramList.end(); ++it)
  {
    alg->setPropertyValue(it.key().toStdString(),it.value().toStdString());
  }
  MantidQt::API::AlgorithmDialog* dlg = createAlgorithmDialog(alg);

  if (algName == "Load") 
  {
    // when loading files, we'll need to update the list of recent files
    // hook up MantidUI::fileDialogAccept() to the LoadDialog dialog accepted() signal
    connect(dlg, SIGNAL(accepted()), this, SLOT(loadFileDialogAccept()));
  }

  if (obs)
  {
    dlg->addAlgorithmObserver(obs);
  }

  dlg->show();
  dlg->raise();
  dlg->activateWindow();
}

/**
* Slot for executing an algorithm.
* @param alg :: Shared pointer to an algorithm to execute with all properties already set.
*/
void MantidUI::executeAlgorithm(Mantid::API::IAlgorithm_sptr alg)
{
  executeAlgorithmAsync(alg);
}

/**
* Execute an algorithm
* @param algName :: The algorithm name
* @param paramList :: A list of algorithm properties to be passed to Algorithm::setProperties
* @param obs :: A pointer to an instance of AlgorithmObserver which will be attached to the finish notification
*/
void MantidUI::executeAlgorithm(const QString & algName, const QString & paramList, Mantid::API::AlgorithmObserver* obs)
{
  //Get latest version of the algorithm
  Mantid::API::IAlgorithm_sptr alg = this->createAlgorithm(algName, -1);
  if( !alg ) return;
  if (obs)
  {
    obs->observeFinish(alg);
  }
  alg->setProperties(paramList.toStdString());
  executeAlgorithmAsync(alg);
}

/**
* This creates an algorithm dialog (the default property entry thingie).
*/
MantidQt::API::AlgorithmDialog*  MantidUI::createAlgorithmDialog(Mantid::API::IAlgorithm_sptr alg)
{
  QHash<QString, QString> presets;
  QStringList enabled;

  //If a property was explicitly set show it as preset in the dialog
  const std::vector<Mantid::Kernel::Property*> props = alg->getProperties();
  std::vector<Mantid::Kernel::Property*>::const_iterator p = props.begin();
  for(; p != props.end(); ++p)
  {
    if ( !(**p).isDefault() )
    {
      QString property_name = QString::fromStdString((**p).name());
      presets.insert(property_name, QString::fromStdString((**p).value()));
      enabled.append(property_name);
    }
  }

  //If a workspace is selected in the dock then set this as a preset for the dialog
  QString selected = getSelectedWorkspaceName();
  if( !selected.isEmpty() )
  {
    QString property_name = findInputWorkspaceProperty(alg);
    if ( !presets.contains(property_name) )
    {
      presets.insert(property_name,selected);
      // Keep it enabled
      enabled.append(property_name);
    }
  }

  //Check if a workspace is selected in the dock and set this as a preference for the input workspace
  //This is an optional message displayed at the top of the GUI.
  QString optional_msg(alg->summary().c_str());

  MantidQt::API::InterfaceManager interfaceManager;
  MantidQt::API::AlgorithmDialog *dlg = interfaceManager.createDialog(alg, m_appWindow, false, presets, optional_msg,enabled);
  return dlg;
}

/**
* Find the first input workspace for an algorithm
* @param algorithm :: A pointer to the algorithm instance
*/
QString MantidUI::findInputWorkspaceProperty(Mantid::API::IAlgorithm_sptr algorithm) const
{
  //Iterate through the properties and find the first input one
  std::vector<Mantid::Kernel::Property*> props = algorithm->getProperties();
  std::vector<Mantid::Kernel::Property*>::const_iterator pend = props.end();
  for(std::vector<Mantid::Kernel::Property*>::const_iterator pitr = props.begin(); pitr != pend; ++pitr)
  {
    Mantid::Kernel::Property *base_prop = *pitr;
    const Mantid::API::IWorkspaceProperty *ws_prop = dynamic_cast<Mantid::API::IWorkspaceProperty*>(base_prop);
    if(ws_prop)
    {
      unsigned int direction = base_prop->direction();
      if (direction == Mantid::Kernel::Direction::Input || direction == Mantid::Kernel::Direction::InOut)
      {
        return QString::fromStdString(base_prop->name());
      }
    }
  }
  return QString();
}

void  MantidUI::copyWorkspacestoVector(const QList<QTreeWidgetItem*> &selectedItems,std::vector<std::string> &inputWSVec)
{
  //iterate through each of the selected workspaces
  QList<QTreeWidgetItem*>::const_iterator itr;
  for(itr=selectedItems.begin();itr!=selectedItems.end();++itr)
  {
    std::string inputWSName=(*itr)->text(0).toStdString();
    inputWSVec.push_back(inputWSName);
  }//end of for loop for input workspaces
}

/**
* Determine if the workspace has one or more UB matrixes on one of it's samples.
* @param wsName
* @return True if present
*/
bool MantidUI::hasUB(const QString& wsName)
{
  const std::string algName("HasUB");
  Mantid::API::IAlgorithm_sptr alg;
  try
  {
    
    alg = Mantid::API::AlgorithmManager::Instance().create(algName);
  } catch (...)
  {
    QMessageBox::critical(appWindow(), "MantidPlot - Algorithm error",
        "Cannot create algorithm " + QString::fromStdString(algName) );
    return false;
  }
  if (!alg)
  {
    return false;
  }

  alg->setLogging(false);
  alg->setPropertyValue("Workspace", wsName.toStdString());
  executeAlgorithmAsync(alg, true);

  bool hasUB = alg->getProperty("HasUB");
  return hasUB;
}

/**
* Clears the UB from the selected workspace
* @param wsName :: selected workspace name
*/
void MantidUI::clearUB(const QStringList& wsName)
{
  const std::string algName("ClearUB");
  const int version = -1;
  for (int i = 0; i < wsName.size(); ++i)
  {
    Mantid::API::IAlgorithm_sptr alg;
    try
    {
      alg = Mantid::API::AlgorithmManager::Instance().create(algName, version);
    }
    catch (...)
    {
      QMessageBox::critical(appWindow(), "MantidPlot - Algorithm error",
        "Cannot create algorithm " + QString::fromStdString(algName) + " version "
        + QString::number(version));
      return;
    }
    if (!alg)
    {
      return;
    }

    alg->setPropertyValue("Workspace", wsName[i].toStdString());
    executeAlgorithmAsync(alg);
  }
}

/**
* Renames selected workspace
* @param wsName :: selected workspace name
*/
void MantidUI::renameWorkspace(QStringList wsName)
{ 
  // If the wsname is blank look for an active window and assume this workspace is
  // the one to rename
  if( wsName.isEmpty() )
  {
    MantidMatrix *matrix = dynamic_cast<MantidMatrix*>(appWindow()->activeWindow());
    if( matrix )
    {
      wsName.append(matrix->workspaceName());
    }
    else
    {
      return;
    }
  }

  // Determine the algorithm
  QString algName("RenameWorkspace"); 
  if(wsName.size() > 1) algName = "RenameWorkspaces";

  QHash<QString,QString> presets;
  if(wsName.size() > 1 )
  {
    presets["InputWorkspaces"] =  wsName.join(",");
  }
  else
  {
    presets["InputWorkspace"] =  wsName[0];
  }
  showAlgorithmDialog(algName, presets);
}

void MantidUI::setFitFunctionBrowser(MantidQt::MantidWidgets::FitPropertyBrowser* newBrowser)
{
  if(newBrowser == NULL)
    m_fitFunction = m_defaultFitFunction;
  else
    m_fitFunction = newBrowser;
}

void MantidUI::groupWorkspaces()
{
  try
  {
    std::string sgrpName("NewGroup");
    QString   qwsGrpName=QString::fromStdString(sgrpName);
    std::vector<std::string> inputWSVec;
    //get selected workspaces
    QList<QTreeWidgetItem*>selectedItems=m_exploreMantid->m_tree->selectedItems();
    if(selectedItems.size()<2)
    {	throw std::runtime_error("Select atleast two workspaces to group ");
    }
    if(Mantid::API::AnalysisDataService::Instance().doesExist(sgrpName))
    {
      if ( QMessageBox::question(appWindow(),"","Workspace "+qwsGrpName+" already exists. Do you want to replace it?",
        QMessageBox::Yes, QMessageBox::No) != QMessageBox::Yes) return;
    }
    //
    copyWorkspacestoVector(selectedItems,inputWSVec);
    std::string algName("GroupWorkspaces");
    Mantid::API::IAlgorithm_sptr alg = Mantid::API::AlgorithmManager::Instance().create(algName,1);
    alg->initialize();
    alg->setProperty("InputWorkspaces",inputWSVec);
    alg->setPropertyValue("OutputWorkspace",sgrpName);
    //execute the algorithm
    bool bStatus =alg->execute();
    if(!bStatus)
    {
      QMessageBox::critical(appWindow(),"MantidPlot - Algorithm error"," Error in GroupWorkspaces algorithm");
    }

  }
  catch(std::invalid_argument &)
  {
    QMessageBox::critical(appWindow(),"MantidPlot - Algorithm error"," Error in GroupWorkspaces algorithm");
  }
  catch(Mantid::Kernel::Exception::NotFoundError&)//if not a valid object in analysis data service
  {
    QMessageBox::critical(appWindow(),"MantidPlot - Algorithm error"," Error in GroupWorkspaces algorithm");
  }
  catch(std::runtime_error& )
  {
    QMessageBox::critical(appWindow(),"MantidPlot - Algorithm error"," Error in GroupWorkspaces algorithm");
  }
  catch(std::exception& )
  {
    QMessageBox::critical(appWindow(),"MantidPlot - Algorithm error"," Error in GroupWorkspaces algorithm");
  }

}
void MantidUI::ungroupWorkspaces()
{
  try
  {
    QList<QTreeWidgetItem*>selectedItems=m_exploreMantid->m_tree->selectedItems();
    if(selectedItems.isEmpty())
    {
      throw std::runtime_error("Select a group workspace to Ungroup.");
    }

    //workspace name
    std::string wsname=selectedItems[0]->text(0).toStdString();

    std::string algName("UnGroupWorkspace");
    Mantid::API::IAlgorithm_sptr alg = Mantid::API::AlgorithmManager::Instance().create(algName,1);
    alg->initialize();
    alg->setProperty("InputWorkspace",wsname);

    //execute the algorithm
    bool bStatus=alg->execute();
    if(!bStatus)
    {
      QMessageBox::critical(appWindow(),"MantidPlot - Algorithm error"," Error in UnGroupWorkspace algorithm");
    }

  }
  catch(std::invalid_argument &)
  {
    QMessageBox::critical(appWindow(),"MantidPlot - Algorithm error"," Error in UnGroupWorkspace algorithm");
  }
  catch(std::runtime_error & )
  {
    QMessageBox::critical(appWindow(),"MantidPlot - Algorithm error"," Error in UnGroupWorkspace algorithm");
  }
  catch(std::exception & )
  {
    QMessageBox::critical(appWindow(),"MantidPlot - Algorithm error"," Error in UnGroupWorkspace algorithm");
  }

}

Mantid::API::IAlgorithm_sptr MantidUI::createAlgorithm(const QString& algName, int version)
{
  emit algorithmAboutToBeCreated(); 
  Mantid::API::IAlgorithm_sptr alg;
  try
  {
    alg = Mantid::API::AlgorithmManager::Instance().create(algName.toStdString(),version);
  }
  catch(...)
  {
    QString message= "Cannot create algorithm \""+ algName + "\"";
    if (version != -1)
    {
      message+= " version "+QString::number(version);
    }
    QMessageBox::warning(appWindow(),"MantidPlot",message);
    alg = Mantid::API::IAlgorithm_sptr();
  }
  return alg;
}

bool MantidUI::executeAlgorithmAsync(Mantid::API::IAlgorithm_sptr alg, const bool wait)
{
  if( wait )
  {
    Poco::ActiveResult<bool> result(alg->executeAsync()); 
    while( !result.available() ) 
    { 
      QCoreApplication::processEvents(); 
    } 
    result.wait();

    try 
    { 
      return result.data(); 
    } 
    catch( Poco::NullPointerException& ) 
    { 
      return false; 
    } 
  }
  else
  {
    try
    {
      alg->executeAsync();
    }
    catch (Poco::NoThreadAvailableException &)
    {
      g_log.error() << "No thread was available to run the " << alg->name() << " algorithm in the background." << std::endl;
      return false;
    }
    return true;
  }
}

/**
* Slot to update the recent files list (from main appWindow) when accepting LoadDialog dialogs
*/
void MantidUI::loadFileDialogAccept()
{
  QObject* sender = QObject::sender();
  MantidQt::API::AlgorithmDialog* dlg = reinterpret_cast<MantidQt::API::AlgorithmDialog*>(sender);
  if (!dlg)
    return;  // should never happen

  QString fn = MantidQt::API::AlgorithmInputHistory::Instance().previousInput("Load", "Filename");
  appWindow()->updateRecentFilesList(fn);
  // recent files list updated. After this point, the Qt signal handler will go to LoadDialog::accept()
}

void MantidUI::handleLoadDAEFinishedNotification(const Poco::AutoPtr<Algorithm::FinishedNotification>& pNf)
{
  std::string wsNAme = pNf->algorithm()->getProperty("OutputWorkspace");
  emit needToCreateLoadDAEMantidMatrix(QString::fromStdString(wsNAme));
}

void MantidUI::createLoadDAEMantidMatrix(const QString& wsQName)
{
  std::string wsName = wsQName.toStdString();
  Workspace_sptr ws = AnalysisDataService::Instance().retrieve(wsName);

  if (ws.use_count() == 0)
  {
    QMessageBox::warning(m_appWindow, tr("Mantid"),
      tr("A workspace with this name already exists.\n")
      , QMessageBox::Ok, QMessageBox::Ok);
    return;
  }

  importMatrixWorkspace(QString::fromStdString(wsName), -1, -1, false, true);

  int updateInterval = m_DAE_map[wsName];
  if (updateInterval > 0)
  {
    IAlgorithm_sptr updater = createAlgorithm("UpdateDAE");
    updater->setPropertyValue("Workspace",wsName);
    updater->setPropertyValue("UpdateRate",QString::number(updateInterval).toStdString());
    executeAlgorithmAsync(updater);
  }
}

void MantidUI::showCritical(const QString& text)
{
  QMessageBox::critical(appWindow(),"Mantid - Error",text);
}

void MantidUI::showAlgMonitor()
{
  m_algMonitor->showDialog();
}

void MantidUI::handleAddWorkspace(Mantid::API::WorkspaceAddNotification_ptr)
{
  emit ADS_updated();
}

void MantidUI::handleReplaceWorkspace(Mantid::API::WorkspaceAfterReplaceNotification_ptr)
{
  emit ADS_updated();
}

void MantidUI::handleDeleteWorkspace(Mantid::API::WorkspacePostDeleteNotification_ptr )
{
  emit ADS_updated();
}

void MantidUI::handleClearADS(Mantid::API::ClearADSNotification_ptr)
{
  emit workspaces_cleared();
}

void MantidUI::handleRenameWorkspace(Mantid::API::WorkspaceRenameNotification_ptr msg)
{
  emit workspace_renamed(QString::fromStdString(msg->objectName()),QString::fromStdString(msg->newObjectName()));
  emit ADS_updated();
}
void MantidUI::handleGroupWorkspaces(Mantid::API::WorkspacesGroupedNotification_ptr)
{
  emit ADS_updated();
}
void MantidUI::handleUnGroupWorkspace(Mantid::API::WorkspaceUnGroupingNotification_ptr)
{
  emit ADS_updated();
}

void MantidUI::handleWorkspaceGroupUpdate(Mantid::API::GroupUpdatedNotification_ptr)
{
  emit ADS_updated();
}

void MantidUI::handleConfigServiceUpdate(Mantid::Kernel::ConfigValChangeNotification_ptr pNf){
  if (pNf->key() == "pythonscripts.directories"){
    // this code ad the filepaths inside the pythonscripts.directories to the 
    // python sys if they are not already there. This is to cope with the requirement
    // at #7097 of letting python scripts usable when downloaded from Script Repository. 
    // This code was added because changing the pythonscripts.directories update the 
    // python path just after restarting MantidPlot.
    QString code = QString("import sys\n"
                           "paths = '%1'\n"
                           "list_of_path = paths.split(';')\n"
                           "if isinstance(list_of_path,str):\n"
                           "  list_of_path = [list_of_path,]\n"
                           "for value in list_of_path:\n"
                           "  if value not in sys.path: sys.path.append(value)\n").arg(QString::fromStdString(pNf->curValue()));
    // run this code silently
    appWindow()->runPythonScript(code, false, true, true);
  }
}

void MantidUI::manageMantidWorkspaces()
{
#ifdef _WIN32
  memoryImage();
#else
  QMessageBox::warning(appWindow(),tr("Mantid Workspace"),tr("Clicked on Manage Workspace"),tr("Ok"),tr("Cancel"),QString(),0,1);
#endif
}

/** Create an instrument window from a named workspace.
*  The window will be returned hidden.
*  @param wsName The name of the workspace for which to generate the instrument view.
*  @param tab    The index of the tab (starting from 0) to initially display (default: 0)
*  @return A pointer to the instrument window widget if created. NULL otherwise.
*/
InstrumentWindow* MantidUI::getInstrumentView(const QString & wsName, int tab)
{
  if( !Mantid::API::AnalysisDataService::Instance().doesExist(wsName.toStdString()) ) return NULL;
  MatrixWorkspace_const_sptr ws = boost::dynamic_pointer_cast<const MatrixWorkspace>(getWorkspace(wsName));
  if (!ws) return NULL;
  QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
  Mantid::Geometry::Instrument_const_sptr instr = ws->getInstrument();
  if (!instr || instr->getName().empty())
  {
    QApplication::restoreOverrideCursor();
    QMessageBox::critical(appWindow(),"MantidPlot - Error","Instrument view cannot be opened");
    return NULL;
  }

  //Need a new window
  const QString windowName(QString("InstrumentWindow:") + wsName);
  InstrumentWindow *insWin = new InstrumentWindow(wsName,QString("Instrument"),appWindow(),windowName);
  try
  {
    insWin->init();
  }
  catch(const std::exception& e)
  {
    QApplication::restoreOverrideCursor();
    QString errorMessage = "Instrument view cannot be created:\n\n" + QString(e.what());
    QMessageBox::critical(appWindow(),"MantidPlot - Error",errorMessage);
    if (insWin)
    {
      appWindow()->closeWindow(insWin);
      insWin->close();
    }
    return NULL;
  }

  insWin->selectTab(tab);

  appWindow()->addMdiSubWindow(insWin);

  connect(insWin, SIGNAL(execMantidAlgorithm(const QString&,const QString&,Mantid::API::AlgorithmObserver*)), this,
    SLOT(executeAlgorithm(const QString&, const QString&,Mantid::API::AlgorithmObserver*)));
  connect(insWin, SIGNAL(execMantidAlgorithm(Mantid::API::IAlgorithm_sptr)), this,
    SLOT(executeAlgorithm(Mantid::API::IAlgorithm_sptr)));

  QApplication::restoreOverrideCursor();
  return insWin;
}


void MantidUI::showMantidInstrument(const QString& wsName)
{
  InstrumentWindow *insWin = getInstrumentView(wsName);
  if (!insWin)
  {
    m_lastShownInstrumentWin = NULL;
    return;
  }

  if (workspacesDockPlot1To1())
  {
    // replace last one
    if (m_lastShownInstrumentWin)
    {
      m_lastShownInstrumentWin->close();
      QPoint p = m_lastShownInstrumentWin->pos();
      delete m_lastShownInstrumentWin;
      insWin->move(p);
    }
  }
  m_lastShownInstrumentWin = insWin;

  if (!insWin->isVisible())
  {
    insWin->show();
  }
}

void MantidUI::showMantidInstrument()
{
  MantidMatrix* m = dynamic_cast<MantidMatrix*>(appWindow()->activeWindow());
  if (!m || !m->isA("MantidMatrix")) 
    return;
  if(!m->workspaceName().isEmpty())
  {
    showMantidInstrument(m->workspaceName());
  }
}

void MantidUI::showMantidInstrumentSelected()
{
  QString wsName = getSelectedWorkspaceName();
  if (!wsName.isEmpty()) showMantidInstrument(wsName);
}

void MantidUI::mantidMenuAboutToShow()
{
  mantidMenu->clear();
  // Ticket #672 Mantid Menu Improvements

  /*mantidMenu->insertItem(tr("&Manage Workspaces"), this, SLOT(manageMantidWorkspaces() ) );
  mantidMenu->insertItem(tr("&Instrument Window"), this, SLOT(showMantidInstrument() ) );
  mantidMenu->insertItem(tr("&Plot Memory Usage"), this, SLOT(manageMantidWorkspaces() ));
  */

  QAction* tstAction = new QAction("&Plot Memory Usage",this);
  connect(tstAction,SIGNAL(triggered()), this, SLOT(manageMantidWorkspaces() ));
  mantidMenu->addAction(tstAction);
}

void MantidUI::insertMenu()
{
  appWindow()->myMenuBar()->insertItem(tr("Man&tid"), mantidMenu);
}

void MantidUI::clearAllMemory()
{
  QMessageBox::StandardButton pressed =
    QMessageBox::question(appWindow(), "MantidPlot", "All workspaces and windows will be removed. Are you sure?", QMessageBox::Ok|QMessageBox::Cancel, QMessageBox::Ok);

  if( pressed != QMessageBox::Ok ) return;

  // Relevant notifications are connected to signals that will close all dependent windows
  Mantid::API::FrameworkManager::Instance().clear();
}


/** Release any free memory back to the system */
void MantidUI::releaseFreeMemory()
{
  // This only does something if TCMalloc is used
  Mantid::API::MemoryManager::Instance().releaseFreeMemory();
}

void MantidUI::saveProject(bool saved)
{
  if( !saved )
  {
    QString savemsg = tr("Save changes to project: <p><b> %1 </b> ?").arg("untitled");
    int result = QMessageBox::information(appWindow(), tr("MantidPlot"), savemsg, tr("Yes"), tr("No"), 0, 2);
    if( result == 0)
      appWindow()->saveProject();
  }
  //close all the windows opened
  foreach( MdiSubWindow* sub_win, appWindow()->windowsList() )
  {
    sub_win->setconfirmcloseFlag(false);
    sub_win->close();
  }
  Mantid::API::FrameworkManager::Instance().clear();
}

void MantidUI::enableSaveNexus(const QString& wsName)
{
  appWindow()->enableSaveNexus(wsName);
}

void MantidUI::disableSaveNexus()
{
  appWindow()->disableSaveNexus();
}


/** This method is sueful for saving the currently loaded workspaces to project file on save.
*  saves the names of all the workspaces loaded into mantid workspace tree
*  into a string and calls save nexus on each workspace to save the data to a nexus file.
* @param workingDir :: -working directory of teh current project
*/
QString MantidUI::saveToString(const std::string& workingDir)
{
  QString wsNames;
  wsNames="<mantidworkspaces>\n";
  wsNames+="WorkspaceNames";
  QTreeWidget *tree=m_exploreMantid->m_tree;
  int count=tree->topLevelItemCount();
  for(int i=0;i<count;++i)
  { 
    QTreeWidgetItem* item=tree->topLevelItem(i);
    QString wsName=item->text(0);
    if (Mantid::API::FrameworkManager::Instance().getWorkspace(wsName.toStdString())->id() == "WorkspaceGroup")
    {
      Mantid::API::WorkspaceGroup_sptr group = boost::dynamic_pointer_cast<Mantid::API::WorkspaceGroup>(Mantid::API::AnalysisDataService::Instance().retrieve(wsName.toStdString()));
      wsNames+="\t";
      //wsName is a group, add it to list and indicate what the group contains by a "[" and end the group with a "]"
      wsNames+=wsName;
      std::vector<std::string> secondLevelItems = group->getNames();
      for(size_t j=0; j<secondLevelItems.size(); j++) //ignore string "WorkspaceGroup at position 0" (start at child '1')
      {
        wsNames+=",";
        wsNames+=QString::fromStdString(secondLevelItems[j]);
        std::string fileName(workingDir + "//" + secondLevelItems[j] + ".nxs");
        //saving to  nexus file
        try
        {
          savedatainNexusFormat(fileName,secondLevelItems[j]);
        }
        catch(...)
        {
        }
      }
    }
    else
    {
      wsNames+="\t";
      wsNames+=wsName;

      std::string fileName(workingDir + "//" + wsName.toStdString() + ".nxs");
      //saving to  nexus file
      try
      {
        savedatainNexusFormat(fileName,wsName.toStdString());
      }
      catch(...)
      {
      }
    }
  }
  wsNames+="\n</mantidworkspaces>\n";
  return wsNames;
}
/**
*  Prepares the Mantid Menu depending on the state of the active MantidMatrix.
*/
void MantidUI::menuMantidMatrixAboutToShow()
{
  menuMantidMatrix->clear();
  MantidMatrix *w = dynamic_cast<MantidMatrix*>(appWindow()->activeWindow());
  //menuMantidMatrix->addAction(actionCopyValues);
  menuMantidMatrix->addAction(actionCopyDetectorsToTable);
  menuMantidMatrix->addSeparator();
  menuMantidMatrix->insertItem(tr("Set &Properties..."), w, SLOT(setMatrixProperties() ) );

  ///
  menuMantidMatrix->addSeparator();
  QAction * action = new QAction("Show instrument",this);
  connect(action,SIGNAL(triggered()),this,SLOT(showMantidInstrument()));
  menuMantidMatrix->addAction(action);

  action = new QAction("Plot spectrum...",this);
  connect(action,SIGNAL(triggered()),m_exploreMantid,SLOT(plotSpectra()));
  menuMantidMatrix->addAction(action);

  action = new QAction("Plot as waterfall",this);
  connect(action,SIGNAL(triggered()),SLOT(plotWholeAsWaterfall()));
  menuMantidMatrix->addAction(action);

  action = new QAction("Sample Logs...", this);
  connect(action,SIGNAL(triggered()),this,SLOT(showLogFileWindow()));
  menuMantidMatrix->addAction(action);

  action = new QAction("Sample Material...", this);
  connect(action,SIGNAL(triggered()),this,SLOT(showSampleMaterialWindow()));
  menuMantidMatrix->addAction(action);

  action = new QAction("Show History", this);
  connect(action,SIGNAL(triggered()),this,SLOT(showAlgorithmHistory()));
  menuMantidMatrix->addAction(action);

  action = new QAction("Save Nexus",this);
  connect(action,SIGNAL(activated()),this,SLOT(saveNexusWorkspace()));
  menuMantidMatrix->addAction(action);

  action = new QAction("Rename",this);
  connect(action,SIGNAL(activated()),this,SLOT(renameWorkspace()));
  menuMantidMatrix->addAction(action);


  //separate delete
  menuMantidMatrix->addSeparator();

  action = new QAction("Delete",this);
  connect(action,SIGNAL(triggered()),m_exploreMantid,SLOT(deleteWorkspaces()));
  menuMantidMatrix->addAction(action);

}

/// Catches the signal from InstrumentWindow to plot a spectrum.
MultiLayer* MantidUI::plotInstrumentSpectrum(const QString& wsName, int spec)
{
  QMessageBox::information(appWindow(),"OK",wsName+" "+QString::number(spec));
  return plotSpectraRange(wsName, spec, spec, MantidQt::DistributionDefault, false);
}

/// Catches the signal from InstrumentWindow to plot a spectrum.
MultiLayer* MantidUI::plotInstrumentSpectrumList(const QString& wsName, std::set<int> spec)
{
  return plot1D(wsName, spec, true, MantidQt::DistributionDefault, false);
}

/**
* Sets the flag that tells the scripting environment that
* a script is currently running
*/
void MantidUI::setIsRunning(bool)
{
  // deprecated
}

/**
* Merge the curves from the two given MultiLayer objects
*/
MultiLayer* MantidUI::mergePlots(MultiLayer* mlayer_1, MultiLayer* mlayer_2)
{
  if( !mlayer_1 ) return NULL;
  if( !mlayer_2 ) return mlayer_1;
  int ncurves_on_two = mlayer_2->activeGraph()->visibleCurves();
  for( int c = 0; c < ncurves_on_two; ++c )
  {
    mlayer_1->insertCurve(mlayer_2, c);
  }

  // Hide the second graph for now as closing it
  // deletes the curves that were associated with it
  mlayer_2->close();

  return mlayer_1;
};

MantidMatrix* MantidUI::getMantidMatrix(const QString& wsName)
{
  QList<MdiSubWindow*> windows = appWindow()->windowsList();
  QListIterator<MdiSubWindow*> itr(windows);
  MantidMatrix* m(0);
  while( itr.hasNext() )
  {
    MdiSubWindow *w = itr.next();
    if( w->isA("MantidMatrix") && w->name() == wsName )
    {
      m = qobject_cast<MantidMatrix*>(w);
    }
  }
  return m;
}

MantidMatrix* MantidUI::newMantidMatrix(const QString& wsName, int start, int end)
{
  return importMatrixWorkspace(wsName, false, false, start, end);
}

bool MantidUI::createScriptInputDialog(const QString & alg_name, const QString & preset_values,
                                       const QString & optional_msg,  const QStringList & enabled,
                                       const QStringList & disabled)
{
  IAlgorithm_sptr alg = AlgorithmManager::Instance().newestInstanceOf(alg_name.toStdString());
  if( !alg )
  {
    return false;
  }

  //PyQt can't pass a dictionary across the boundary as a dictionary can contain arbitrary data types
  QHash<QString,QString> presets;
  QStringList chopped = preset_values.split('|', QString::SkipEmptyParts);
  QStringListIterator itr(chopped);
  while( itr.hasNext() )
  {
    QString namevalue = itr.next();
    QString name = namevalue.section('=', 0, 0);
    // Simplified removes trims from start and end and replaces all n counts of whitespace with a single whitespace
    QString value = namevalue.section('=', 1, 1).simplified();
    presets.insert(name, value);
  }

  MantidQt::API::InterfaceManager interfaceManager;
  MantidQt::API::AlgorithmDialog *dlg =
    interfaceManager.createDialog(alg, m_appWindow->getScriptWindowHandle(),
                                  true, presets, optional_msg, enabled, disabled);
  return (dlg->exec() == QDialog::Accepted);
}

/** Displays a string in a Qtiplot table
*  @param logName :: the title of the table is based on this
*  @param data :: the string to display
*/
void MantidUI::importString(const QString &logName, const QString &data)
{
  importString(logName,data,QString(""));
}

/** Displays a string in a Qtiplot table
*  @param logName :: the title of the table is based on this
*  @param data :: the string to display
*  @param sep :: the seperator character
*  @param wsName :: add workspace name to the table window title bar, defaults to logname if left blank
*/
void MantidUI::importString(const QString &logName, const QString &data, const QString &sep, const QString &wsName)
{
  QStringList loglines =  QStringList(data);
  if (sep.length() > 0)
  {
    loglines = data.split(sep, QString::SkipEmptyParts);
  }

  Table* t = new Table(appWindow()->scriptingEnv(), loglines.size(), 1, "", appWindow(), 0);
  if( !t ) return;
  //Have to replace "_" since the legend widget uses them to separate things
  QString label;
  label = logName;
  formatLogName(label, wsName);

  appWindow()->initTable(t, appWindow()->generateUniqueName(label + "-"));
  t->setColName(0, "Log entry");
  t->setReadOnlyColumn(0, true); //Read-only

  for (int i=0; i<loglines.size(); ++i)
  {
    t->setText(i, 0, loglines[i]);
  }

  //Show table
  t->resize(2*t->table()->horizontalHeader()->sectionSize(0) + 55,
    (QMIN(10,1)+1)*t->table()->verticalHeader()->sectionSize(0)+100);
  t->setAttribute(Qt::WA_DeleteOnClose);
  t->showNormal();
}
/** Displays a string in a Qtiplot table
*  @param logName :: the title of the table is based on this
*  @param data :: a formated string with the time series data to display
*  @param wsName :: add workspace name to the table window title bar, defaults to logname if left blank
*/
void MantidUI::importStrSeriesLog(const QString &logName, const QString &data, const QString &wsName)
{
  QStringList loglines = data.split("\n", QString::SkipEmptyParts);

  int rowcount(loglines.count());
  Table* t = new Table(appWindow()->scriptingEnv(), rowcount, 2, "", appWindow(), 0);
  if( !t ) return;
  QString label;
  label = logName;
  formatLogName(label, wsName);

  appWindow()->initTable(t, appWindow()->generateUniqueName(label + "-"));
  t->setColName(0, "Time");
  t->setColumnType(0, Table::Time);
  t->setTimeFormat("HH:mm:ss", 0, false);
  t->setColName(1, label.section("-",1));

  // Make both columns read-only
  t->setReadOnlyColumn(0, true);
  t->setReadOnlyColumn(1, true);

  QStringList::const_iterator sEnd = loglines.end();
  int row(0);
  for( QStringList::const_iterator sItr = loglines.begin(); sItr != sEnd; ++sItr, ++row )
  {
    QStringList ts = (*sItr).split(QRegExp("\\s+"));
    t->setText(row, 0, ts[1]);
    QStringList ds(ts);
    ds.removeFirst();// remove date
    ds.removeFirst();// and time
    t->setText(row, 1, ds.join(" "));
  }

  //Show table
  t->resize(2*t->table()->horizontalHeader()->sectionSize(0) + 55,
    (QMIN(10,rowcount)+1)*t->table()->verticalHeader()->sectionSize(0)+100);
  t->setAttribute(Qt::WA_DeleteOnClose);
  t->showNormal();
}

//------------------------------------------------------------------------------------------------
/**  Import a numeric log data. It will be shown in a graph and copied into a table
* @param wsName :: The workspace name which log data will be imported
* @param logName :: The name of the log property to import
* @param filter :: Filter flag telling how to filter the log data.
* - 0 means no filtering
* - 1 filter by running status
* - 2 filter by period
* - 3 filter by status & period
*/
void MantidUI::importNumSeriesLog(const QString &wsName, const QString &logName, int filter)
{
  //if you need to add a final filter valure to the end of the filter to match the extent of the data, then set this to the index of the row to add the value
  int addFinalFilterValueIndex = 0;
  Mantid::Kernel::DateAndTime lastFilterTime;

  MatrixWorkspace_const_sptr ws = boost::dynamic_pointer_cast<const MatrixWorkspace>(getWorkspace(wsName));
  if (!ws) return;

  Mantid::Kernel::Property * logData =ws->run().getLogData(logName.toStdString());
  if (!logData) return;

  Mantid::Kernel::LogFilter flt(logData);

  //Get a map of time/value. This greatly speeds up display.
  // NOTE: valueAsMap() skips repeated values.
  std::map<DateAndTime, double> time_value_map = flt.data()->valueAsCorrectMap();
  int rowcount = static_cast<int>(time_value_map.size());
  int colCount = 2;

  Table* t = new Table(appWindow()->scriptingEnv(), rowcount, colCount, "", appWindow(), 0);
  if( !t ) return;
  //Have to replace "_" since the legend widget uses them to separate things
  QString label;
  label = logName;
  formatLogName(label, wsName);

  //Get the starting time of the log.
  Mantid::Kernel::DateAndTime startTime;
  //Toggle to switch between using the real date or the change in seconds.
  bool useAbsoluteDate = false;

  if (!time_value_map.empty())
  {
    try {
      startTime = ws->run().startTime();
    } catch (std::runtime_error&) {
      // This means the start time is missing, use absolute times instead
      useAbsoluteDate = true;
    }
  }

  //Make a unique title, and put in the start time of the log
  QString title = label + QString::fromStdString( " (" + startTime.toSimpleString() + ")" );
  appWindow()->initTable(t, appWindow()->generateUniqueName(title));

  // Make both columns read-only
  t->setReadOnlyColumn(0, true);
  t->setReadOnlyColumn(1, true);

  if (useAbsoluteDate)
  {
    // --------- Date
    t->setColName(0, "Time");
    t->setColumnType(0, Table::Date);
    t->setDateFormat("yyyy-MMM-dd HH:mm:ss.ffffff", 0, false);
  }
  else
  {
    //Seconds offset
    t->setColName(0, "Time (sec)");
    t->setColumnType(0, Table::Numeric); //six digits after 0
    t->setNumericPrecision(6); //six digits after 0
  }

  //Make the column header with the units, if any
  QString column1 = label.section("-",1);
  if (logData->units() != "")
    column1 = column1 + QString::fromStdString(" (in " + logData->units() + ")");
  t->setColName(1, column1);

  int iValueCurve = 0;
  int iFilterCurve = 1;

  // Applying filters
  if (filter > 0)
  {
    Mantid::Kernel::TimeSeriesProperty<bool>* f = 0;
    if (filter == 1 || filter ==3)
    {
      try
      {
        f = dynamic_cast<Mantid::Kernel::TimeSeriesProperty<bool> *>(ws->run().getLogData("running"));
        if (f) flt.addFilter(*f);
        else
        {
          t->setconfirmcloseFlag(false);
          t->setAttribute(Qt::WA_DeleteOnClose);
          t->close();
          importNumSeriesLog(wsName,logName,0);
          return;
        }
      }
      catch(...)
      {
        t->setconfirmcloseFlag(false);
        t->setAttribute(Qt::WA_DeleteOnClose);
        t->close();
        importNumSeriesLog(wsName,logName,0);
        return;
      }
    }

    if (filter == 2 || filter ==3)
    {
      std::vector<Mantid::Kernel::Property*> ps =ws->run().getLogData();
      for(std::vector<Mantid::Kernel::Property*>::const_iterator it=ps.begin();it!=ps.end();++it)
        if ((*it)->name().find("period ") == 0)
        {
          try
          {
            f = dynamic_cast<Mantid::Kernel::TimeSeriesProperty<bool> *>(*it);
            if (f) flt.addFilter(*f);
            else
            {
              importNumSeriesLog(wsName,logName,0);
              return;
            }
          }
          catch(...)
          {
            importNumSeriesLog(wsName,logName,0);
            return;
          }

          break;
        }
    }


    if (flt.filter())
    {
      //Valid filter was found
      t->addColumns(2);
      t->setColName(2, "FTime");

      if (useAbsoluteDate)
      {
        t->setColumnType(2, Table::Date);
        t->setDateFormat("yyyy-MMM-dd HH:mm:ss", 2, false); //This is the format of the date column
      }
      else
      {
        t->setColumnType(2, Table::Numeric); //six digits after 0
        t->setNumericPrecision(6); //six digits after 0
      }

      t->setColPlotDesignation(2,Table::X);
      t->setColName(3, "Filter");

      if (flt.filter()->size() > rowcount)
      {
        t->addRows(flt.filter()->size() - rowcount);
      }

      if (flt.data()->size() > rowcount)
      {
        t->addRows(flt.data()->size() - rowcount);
      }

      for(int i=0;i<flt.filter()->size();i++)
      {
        if (flt.filter()->nthInterval(i).begin() > 0) //protect against bizarre values we sometimes get
        {
          std::string time_string = extractLogTime(flt.filter()->nthInterval(i).begin(),useAbsoluteDate,startTime);

          t->setText(i,2,QString::fromStdString(time_string));
          t->setCell(i,3,!flt.filter()->nthValue(i));
          if((i+1==flt.filter()->size()) && (!flt.filter()->nthValue(i))) //last filter value and set to be filtering
          {
            addFinalFilterValueIndex = i+1;
            lastFilterTime = flt.filter()->nthInterval(i).begin();
          }
        }
      }

      iValueCurve = 1;
      iFilterCurve = 0;

    } //end (valid filter exists)

  }

  Mantid::Kernel::DateAndTime lastTime;
  double lastValue = 0;

  //Iterate through the time-value map.
  std::map<DateAndTime, double>::iterator it = time_value_map.begin();
  if (it!=time_value_map.end())
  {
    for (int i = 0; it!=time_value_map.end(); ++i,++it)
    {
      lastTime = it->first;
      lastValue = it->second;

      std::string time_string = extractLogTime(lastTime,useAbsoluteDate,startTime);

      t->setText(i,0,QString::fromStdString(time_string));
      t->setCell(i,1,lastValue);
    }
  }

  try
  {
    //Set the filter strings
    if (filter && flt.filter() && lastTime < flt.filter()->lastTime())
    {
      rowcount = static_cast<int>(time_value_map.size());
      if (rowcount == t->numRows()) t->addRows(1);

      std::string time_string = extractLogTime(flt.filter()->lastTime(),useAbsoluteDate,startTime);

      t->setText(rowcount,0,QString::fromStdString(time_string));
      t->setCell(rowcount,1,lastValue);
    }
  }
  catch(...)
  {
  }

  //add a final filter value if needed and the data exceed the filter range
  if ((addFinalFilterValueIndex > 0) && (lastFilterTime < lastTime))
  { 
    if (addFinalFilterValueIndex >= t->numRows())
    {
      t->addRows(1);
    }
    std::string end_string = extractLogTime(lastTime,useAbsoluteDate,startTime);
    t->setText(addFinalFilterValueIndex,2,QString::fromStdString(end_string));
    t->setCell(addFinalFilterValueIndex,3,1); // only need to add it if filter =1
  }

  //Show table

  t->resize(2*t->table()->horizontalHeader()->sectionSize(0) + 55,
    (QMIN(10,t->numRows())+1)*t->table()->verticalHeader()->sectionSize(0)+100);
  //t->askOnCloseEvent(false);
  t->setAttribute(Qt::WA_DeleteOnClose);
  t->showNormal();

  // Do not create graph if there is only one value in the table or using absolute dates
  if (t->numRows() < 2 || useAbsoluteDate ) return;

  QStringList colNames;
  if (filter && flt.filter())
  {
    colNames <<t->colName(3);
  }
  colNames << t->colName(1);
  MultiLayer *ml = appWindow()->multilayerPlot(t,colNames,Graph::Line);
  // ml->askOnCloseEvent(false);
  ml->setAttribute(Qt::WA_DeleteOnClose);

  Graph* g = ml->activeGraph();

  // Set x-axis label format
  if (useAbsoluteDate)
  {
    Mantid::Kernel::DateAndTime label_as_ptime = flt.data()->nthInterval(0).begin();
    QDateTime dt = QDateTime::fromTime_t( uint(label_as_ptime.to_localtime_t()) );
    QString format = dt.toString(Qt::ISODate) + ";HH:mm:ss";
    g->setLabelsDateTimeFormat(2,ScaleDraw::Date,format);
  }
  else
  {
    //Make the x-axis a numeric format, 0 decimals
    g->setLabelsNumericFormat(2,1,0, "");
  }

  // Set style #3 (HorizontalSteps) for curve iValueCurve
  g->setCurveStyle(iValueCurve,3);
  QPen pn = QPen(Qt::black);
  g->setCurvePen(iValueCurve, pn);

  if (filter && flt.filter())
  {
    QwtPlotCurve *c = g->curve(iFilterCurve);
    // Set the right axis as Y axis for the filter curve.
    c->setAxis(2,1);
    // Set style #3 (HorizontalSteps) for curve 1
    // Set scale of right Y-axis (#3) from 0 to 1
    g->setCurveStyle(iFilterCurve,3);
    g->setScale(3,0,1);
    // Fill area under the curve with a pattern
    QBrush br = QBrush(Qt::gray, Qt::Dense5Pattern);
    g->setCurveBrush(iFilterCurve, br);
    // Set line colour
    QPen pn = QPen(Qt::gray);
    g->setCurvePen(iFilterCurve, pn);
  }
  g->setXAxisTitle(t->colLabel(0));
  g->setYAxisTitle(t->colLabel(1).section(".",0,0));
  g->setTitle(label);
  g->setAutoScale();

  ml->showNormal();

}

/** Format a log name for a title bar
@param[out] label :: the QString that will hold the caption
@param[in] wsName :: the workspace name
*/
void MantidUI::formatLogName(QString &label, const QString &wsName)
{
  label.replace("_","-");
  if (!wsName.isEmpty())
  {
    label = wsName + "-" + label;
  }
}

std::string  MantidUI::extractLogTime(Mantid::Kernel::DateAndTime value,bool useAbsoluteDate, Mantid::Kernel::DateAndTime start)
{
  std::string time_string;
  if (useAbsoluteDate)
  {
    //Convert time into string
    time_string = value.toSimpleString();
  }
  else
  {
    //How many seconds elapsed?
    Mantid::Kernel::time_duration elapsed = value - start;
    double seconds = Mantid::Kernel::DateAndTime::secondsFromDuration(elapsed);

    //Output with 6 decimal points
    std::ostringstream oss;
    oss.precision(6);
    oss << std::fixed << seconds;
    time_string = oss.str();
  }
  return time_string;
}

void MantidUI::showLogFileWindow()
{
  //Need a new window to display entries
  MantidSampleLogDialog *dlg = new MantidSampleLogDialog(getSelectedWorkspaceName(), this);
  dlg->setModal(false);
  dlg->setAttribute(Qt::WA_DeleteOnClose);
  dlg->show();
  dlg->setFocus();
}

void MantidUI::showSampleMaterialWindow()
{
  MantidSampleMaterialDialog *dlg = new MantidSampleMaterialDialog(getSelectedWorkspaceName(), this);
  dlg->setModal(false);
  dlg->setAttribute(Qt::WA_DeleteOnClose);
  dlg->show();
  dlg->setFocus();
  dlg->updateMaterial();
}

//  *****      Plotting Methods     *****  //

/** Create a Table form specified spectra in a MatrixWorkspace
@param tableName :: Table name
@param workspaceName :: Shared pointer to the workspace
@param indexList :: A list of spectra indices to go to the table
@param errs :: If true include the errors into the table
@param binCentres :: If true the X column will contain the bin centres, i.e. (x_i+1 + x_i)/2.
If false the Y values will be in the same row with the left bin boundaries.
If the workspace is not a histogram the parameter is ignored.
*/
Table* MantidUI::createTableFromSpectraList(const QString& tableName, const QString& workspaceName, QList<int> indexList, bool errs, bool binCentres)
{
  MatrixWorkspace_const_sptr workspace =
    boost::dynamic_pointer_cast<const MatrixWorkspace>(getWorkspace(workspaceName));
  if (!workspace)
  {
    throw std::invalid_argument(workspaceName.toStdString()+" is not a Matrix Workspace.");
  }

  int nspec = static_cast<int>(workspace->getNumberHistograms());
  //Loop through the list of index and remove all the indexes that are out of range

  for(QList<int>::iterator it=indexList.begin();it!=indexList.end();)
  {
    if ((*it) > nspec || (*it) < 0)
    {
      // erase moves iterator to next position
      it = indexList.erase(it);
    }
    else
    {
      ++it;
    }
  }
  if ( indexList.empty() ) return 0;

  int c = errs?2:1;
  int numRows = static_cast<int>(workspace->blocksize());
  bool isHistogram = workspace->isHistogramData();
  int no_cols = static_cast<int>(indexList.size());
  Table* t = new Table(appWindow()->scriptingEnv(), numRows, (1+c)*no_cols, "", appWindow(), 0);
  appWindow()->initTable(t, appWindow()->generateUniqueName(tableName+"-"));
  // t->askOnCloseEvent(false);

  for(int i=0;i < no_cols; i++)
  {
    const Mantid::MantidVec& dataX = workspace->readX(indexList[i]);
    const Mantid::MantidVec& dataY = workspace->readY(indexList[i]);
    const Mantid::MantidVec& dataE = workspace->readE(indexList[i]);

    const int kY =(c+1)*i+1;
    const int kX=(c+1)*i;
    int kErr = 0;
    t->setColName(kY,"YS"+QString::number(indexList[i]));
    t->setColName(kX,"XS"+QString::number(indexList[i]));
    t->setColPlotDesignation(kX,Table::X);
    if (errs)
    {
      kErr=(c+1)*i+2;
      t->setColPlotDesignation(kErr,Table::yErr);
      t->setColName(kErr,"ES"+QString::number(indexList[i]));
    }
    for(int j=0;j<numRows;j++)
    {
      if (isHistogram && binCentres)
      {
        t->setCell(j,kX,( dataX[j] + dataX[j+1] )/2);
      }
      else
      {
        t->setCell(j,kX,dataX[j]);
      }
      t->setCell(j,kY,dataY[j]);

      if (errs) t->setCell(j,kErr,dataE[j]);
    }
    if (isHistogram && (!binCentres))
    {
      int iRow = numRows;
      t->addRows(1);
      if (i == 0) t->setCell(iRow,0,dataX[iRow]);
      t->setCell(iRow,kY,0);
      if (errs) t->setCell(iRow,kErr,0);
    }
  }

  return t;
}

/** Creates a Qtiplot Table from selected spectra of MantidMatrix m.
The columns are: 1st column is x-values from the first selected spectrum,
2nd column is y-values of the first spectrum. Depending on value of errs
the 3rd column contains either first spectrum errors (errs == true) or
y-values of the second spectrum (errs == false). Consecutive columns have
y-values and errors (if errs is true) of the following spectra. If visible == true
the table is made visible in Qtiplot.

The name of a Y column is "Y"+QString\:\:number(i), where i is the row in the MantidMatrix,
not the spectrum index in the workspace.

*/
Table* MantidUI::createTableFromSelectedRows(MantidMatrix *m, bool errs, bool binCentres)
{
  const QList<int>& indexList = m->getSelectedRows();
  if (indexList.empty()) return NULL;

  return createTableFromSpectraList(m->name(), QString::fromStdString(m->workspace()->name()),
    indexList, errs, binCentres);
}

/**  Create a 1d graph from a Table.
@param t :: Pointer to the Table.
@param type :: Type of the curve. Possible values are:
- Graph::Line
- Graph::Scatter
- Graph::LineSymbols
- Graph::HorizontalSteps
*/
MultiLayer* MantidUI::createGraphFromTable(Table* t, int type)
{
  if (!t) return NULL;
  QStringList  lst=t->colNames();
  QStringList::const_iterator itr;
  for (itr=lst.begin();itr!=lst.end();++itr)
  {
    //remove the X names from the column list and pass the X removed list
    //to multilayerPlot
    QString str=(*itr);
    if(str.contains("XS",Qt::CaseInsensitive))
    {
      int index=lst.indexOf(str);
      lst.removeAt(index);
    }
  }

  MultiLayer* ml = appWindow()->multilayerPlot(t,lst,Graph::Line);
  Graph *g = ml->activeGraph();
  appWindow()->polishGraph(g,type);
  for(int i=0;i<g->curves();i++)
    g->setCurveStyle(i,type);

  return ml;
}

/** Set properties of a 1d graph which plots bin data from a workspace.
@param ml :: MultiLayer plot with the graph
@param Name :: Name of the graph
@param workspace :: The workspace
*/
void MantidUI::setUpBinGraph(MultiLayer* ml, const QString& Name, Mantid::API::MatrixWorkspace_const_sptr workspace)
{
  Graph* g = ml->activeGraph();
  g->setTitle(tr("Workspace ")+Name);
  QString xtitle;
  if (workspace->axes() > 1)   // Protection against calling this on 1D/single value workspaces
  {
    xtitle = MantidQt::API::PlotAxis(*workspace, 1).title();
  }
  g->setXAxisTitle(xtitle);
  g->setYAxisTitle(MantidQt::API::PlotAxis(*workspace).title());
}

/**
Plots the spectra from the given workspaces
@param ws_names :: List of ws names to plot
@param indexList :: List of indices to plot for each workspace
@param spectrumPlot :: True if indices should be interpreted as row indices
@param errs :: If true include the errors on the graph
@param style :: Curve style for plot
@param plotWindow :: Window to plot to. If NULL a new one will be created
@param clearWindow :: Whether to clear specified plotWindow before plotting. Ignored if plotWindow == NULL
*/
MultiLayer* MantidUI::plot1D(const QStringList& ws_names, const QList<int>& indexList, bool spectrumPlot, bool errs,
                             Graph::CurveType style, MultiLayer* plotWindow, bool clearWindow)
{
  // Convert the list into a map (with the same workspace as key in each case)
  QMultiMap<QString,int> pairs;
  QListIterator<QString> ws_itr(ws_names);
  ws_itr.toBack();
  QListIterator<int> spec_itr(indexList);
  spec_itr.toBack();

  // Need to iterate through the set in reverse order to get the curves in the correct order on the plot
  while( ws_itr.hasPrevious() )
  {
    QString workspace_name = ws_itr.previous();
    while( spec_itr.hasPrevious() )
    {
      pairs.insert(workspace_name, spec_itr.previous());
    }
    //Reset spectrum index pointer
    spec_itr.toBack();
  }

  // Pass over to the overloaded method
  return plot1D(pairs,spectrumPlot,MantidQt::DistributionDefault, errs,style,plotWindow, clearWindow);
}
/** Create a 1D graph from the specified list of workspaces/spectra.
@param toPlot :: Map of form ws -> [spectra_list]
@param spectrumPlot :: True if indices should be interpreted as row indices
@param distr :: if true, workspace plot as y data/bin width
@param errs :: If true include the errors on the graph
@param plotWindow :: Window to plot to. If NULL a new one will be created
@param clearWindow :: Whether to clear specified plotWindow before plotting. Ignored if plotWindow == NULL
@return NULL if failure. Otherwise, if plotWindow == NULL - created window, if not NULL - plotWindow
*/
MultiLayer* MantidUI::plot1D(const QMultiMap<QString, set<int> >& toPlot, bool spectrumPlot,
                             MantidQt::DistributionFlag distr, bool errs,
                             MultiLayer* plotWindow, bool clearWindow)
{
  // Convert the list into a map (with the same workspace as key in each case)
  QMultiMap<QString,int> pairs;
  // Need to iterate through the workspaces
  QMultiMap<QString,std::set<int> >::const_iterator it;
  for (it = toPlot.constBegin(); it != toPlot.constEnd(); ++it)
  {
    std::set<int>::const_reverse_iterator itSet;
    for (itSet = it->rbegin(); itSet != it->rend(); ++itSet)
    {
      pairs.insert(it.key(),*itSet);
    }
  }

  // Pass over to the overloaded method
  return plot1D(pairs,spectrumPlot,distr,errs,Graph::Unspecified,plotWindow, clearWindow);
}

/** Create a 1d graph from the specified spectra in a MatrixWorkspace
@param wsName :: Workspace name
@param indexList :: List of indices to plot for each workspace
@param spectrumPlot :: True if indices should be interpreted as row indices
@param distr :: if true, workspace plot as y data/bin width
@param errs :: If true include the errors on the graph
@param plotWindow :: Window to plot to. If NULL a new one will be created
@param clearWindow :: Whether to clear specified plotWindow before plotting. Ignored if plotWindow == NULL
@return NULL if failure. Otherwise, if plotWindow == NULL - created window, if not NULL - plotWindow
*/
MultiLayer* MantidUI::plot1D(const QString& wsName, const std::set<int>& indexList, bool spectrumPlot,
  MantidQt::DistributionFlag distr, bool errs, MultiLayer* plotWindow, bool clearWindow)
{
  // Convert the list into a map (with the same workspace as key in each case)
  QMultiMap<QString,int> pairs;
  // Need to iterate through the set in reverse order
  std::set<int>::const_reverse_iterator it;
  for (it = indexList.rbegin(); it != indexList.rend(); ++it)
  {
    pairs.insert(wsName,*it);
  }

  // Pass over to the overloaded method
  return plot1D(pairs,spectrumPlot,distr,errs,Graph::Unspecified,plotWindow, clearWindow);
}

/** Create a 1d graph form a set of workspace-spectrum pairs
@param toPlot :: A list of workspace/spectra to be shown in the graph
@param spectrumPlot :: True if indices should be interpreted as row indices
@param distr :: if true, workspace plot as y data/bin width
@param errs :: If true include the errors to the graph
@param style :: curve style for plot
@param plotWindow :: Window to plot to. If NULL a new one will be created
@param clearWindow :: Whether to clear specified plotWindow before plotting. Ignored if plotWindow == NULL
@return NULL if failure. Otherwise, if plotWindow == NULL - created window, if not NULL - plotWindow
*/
MultiLayer* MantidUI::plot1D(const QMultiMap<QString,int>& toPlot, bool spectrumPlot,
                             MantidQt::DistributionFlag distr, bool errs,
                             Graph::CurveType style, MultiLayer* plotWindow, bool clearWindow)
{
  if(toPlot.size() == 0) return NULL;

  if (toPlot.size() > 10)
  {
    QMessageBox ask(appWindow());
    QAbstractButton *confirmButton = ask.addButton(tr("Confirm"), QMessageBox::ActionRole);
    ask.addButton(tr("Cancel"), QMessageBox::ActionRole);
    ask.setText("You selected "+QString::number(toPlot.size())+" spectra to plot. "
      "Are you sure you want to plot this many?");
    ask.setIcon(QMessageBox::Question);
    ask.exec();
    if (ask.clickedButton() != confirmButton) return NULL;
  }

  QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));

  const QString& firstWsName = toPlot.constBegin().key();;
  QString plotTitle;
  // If the first workspace selected in the tree is a WorkspaceGroup,
  // use its name directly, rather than the first in the list 'toPlot'
  // (which will be the first workspace included in the group - not
  // the best title).
  const QString& sel = m_exploreMantid->getSelectedWorkspaceName();
  WorkspaceGroup_const_sptr gWs;
  if (!sel.isEmpty() && AnalysisDataService::Instance().doesExist(sel.toStdString()))
  {
    try
    {
      gWs = boost::dynamic_pointer_cast<const WorkspaceGroup>
        (Mantid::API::AnalysisDataService::Instance().retrieve(sel.toStdString()));
    }
    catch(std::exception&)
    {
      // can happen, nothing to worry about
      gWs = WorkspaceGroup_const_sptr();  // make sure, anyway
    }
  }
  if (gWs)
  {
    plotTitle = sel;
  }
  else
  {
    plotTitle = firstWsName;
  }

  // Limit to 1 window for this type of plot -> reuse plot/graph window
  if(workspacesDockPlot1To1())
  {
    if (m_lastShown1DPlotWin)
    {
      plotWindow = m_lastShown1DPlotWin;
      clearWindow = true;
    }
  }
  bool isGraphNew = false;
  MultiLayer* ml = appWindow()->prepareMultiLayer(isGraphNew, plotWindow, plotTitle, clearWindow);
  ml->setName(appWindow()->generateUniqueName(plotTitle + "-"));
  m_lastShown1DPlotWin = ml;

  // Do we plot a distribution or not
  bool plotAsDistribution(false);
  if(distr == MantidQt::DistributionDefault)
  {
   plotAsDistribution = appWindow()->autoDistribution1D;
  }
  else
  {
    plotAsDistribution = (distr == MantidQt::DistributionTrue);
  }
  
  // Try to add curves to the plot
  Graph *g = ml->activeGraph();
  g->setDistribution(plotAsDistribution);
  MantidMatrixCurve::IndexDir indexType = (spectrumPlot) ? MantidMatrixCurve::Spectrum : MantidMatrixCurve::Bin;
  MantidMatrixCurve* firstCurve(NULL);
  for(QMultiMap<QString,int>::const_iterator it=toPlot.begin();it!=toPlot.end();++it)
  {
    try
    {
      auto * wsCurve = new MantidMatrixCurve(it.key(),g,it.value(),indexType,errs,plotAsDistribution,style);
      if(!firstCurve) firstCurve = wsCurve;
    } 
    catch (Mantid::Kernel::Exception::NotFoundError&) 
    {
      g_log.warning() << "Workspace " << it.key().toStdString() << " not found" << std::endl;
    }
    catch (std::exception& ex)
    {
      g_log.warning() << ex.what() << std::endl;
    }
  }

  if(!isGraphNew)
  {
    // Replot graph is we've added curves to existing one
    g->replot();
  }
  else
  {
    if(!firstCurve)
    {
      QApplication::restoreOverrideCursor();
      return NULL;
    }

    g->setXAxisTitle(firstCurve->mantidData()->getXAxisLabel());
    g->setYAxisTitle(firstCurve->mantidData()->getYAxisLabel());
    g->setAutoScale();
    /* The 'setAutoScale' above is needed to make sure that the plot initially encompasses all the
     * data points. However, this has the side-effect suggested by its name: all the axes become
     * auto-scaling if the data changes. If, in the plot preferences, autoscaling has been disabled
     * the the next line re-fixes the axes
     */
    if ( ! appWindow()->autoscale2DPlots )
      g->enableAutoscaling(false);

    // This deals with the case where the X-values are not in order. In general, this shouldn't
    // happen, but it does apparently with some muon analyses.
    g->checkValuesInAxisRange(firstCurve);
  }

  // Check if window does not contain any curves and should be closed
  ml->maybeNeedToClose();

  QApplication::restoreOverrideCursor();
  return ml;
}

/**
* Draw a color fill plot for each of the listed workspaces. Unfortunately the plotting is 
* initimately linked to MantidMatrix so that one of these needs to be created first
* @param ui :: the sequential fitting UI form
* @param fitbrowser :: pointer to the fit property browser
*/
void MantidUI::showSequentialPlot(Ui::SequentialFitDialog* ui, MantidQt::MantidWidgets::FitPropertyBrowser* fitbrowser)
{
  std::string wsName = fitbrowser->outputName();
  Mantid::API::ITableWorkspace_sptr ws = boost::dynamic_pointer_cast<Mantid::API::ITableWorkspace>(
    Mantid::API::AnalysisDataService::Instance().retrieve(wsName) );
  if (ws)
  {
    if ((ws->columnCount() - 1)/2 != fitbrowser->compositeFunction()->nParams()) return;
    Table *t = importTableWorkspace(QString::fromStdString(wsName));
    if (!t) return;
    QString parName;
    if (fitbrowser->compositeFunction()->nFunctions() == 1)
    {
      size_t i = fitbrowser->compositeFunction()->parameterIndex(ui->cbParameter->currentText().toStdString());
      parName = QString::fromStdString(fitbrowser->compositeFunction()->getFunction(0)->parameterName(i));
    }
    else
    {
      parName = ui->cbParameter->currentText();
    }
    QStringList colNames;
    colNames << t->name() + "_" + parName << t->name() + "_" + parName + "_Err";
    MultiLayer* ml = appWindow()->multilayerPlot(t,colNames,ui->cbCurveType->currentIndex());
    // set plot titles
    Graph* g = ml->activeGraph();
    if (g)
    {
      if (ui->ckbLogPlot->isChecked())
      {
        g->setXAxisTitle(ui->cbLogValue->currentText());
      }
      else
      {
        g->setXAxisTitle("Spectra");
      }
      g->setYAxisTitle(parName);
      g->setTitle("");
    }
  }
}

/**
* Draw a color fill plot for each of the listed workspaces. Unfortunately the plotting is 
* initimately linked to MantidMatrix so that one of these needs to be created first
* @param wsNames :: For each workspace listed create a 2D colorfill plot 
* @param curveType :: The curve type for each of the plots
*/
void MantidUI::drawColorFillPlots(const QStringList & wsNames, Graph::CurveType curveType)
{
  for( QStringList::const_iterator cit = wsNames.begin(); cit != wsNames.end(); ++cit )
  {
    this->drawSingleColorFillPlot(*cit, curveType);
  }
}

/**
* Draw a single ColorFill plot for the named workspace
* @param wsName :: The name of the workspace which provides data for the plot
* @param curveType :: The type of curve
* @param window :: An optional pointer to a plot window. If not NULL the window is cleared
*                      and reused
* @returns A pointer to the created plot
*/
MultiLayer* MantidUI::drawSingleColorFillPlot(const QString & wsName, Graph::CurveType curveType,
                                              MultiLayer* window)
{
  auto workspace = boost::dynamic_pointer_cast<const Mantid::API::MatrixWorkspace>(getWorkspace(wsName));
  if(!workspace) return NULL;

  QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));

  bool reusePlots = workspacesDockPlot1To1();
  if( (!reusePlots && NULL == window) ||
      (reusePlots && !m_lastShownColorFillWin) ) // needs to create a new window
  {
    try
    {
      window = appWindow()->multilayerPlot(appWindow()->generateUniqueName( wsName + "-"));
    }
    catch(std::runtime_error& e)
    {
      m_lastShownColorFillWin = NULL;
      g_log.error() << "Could not create color fill plot: " << e.what() << "\n";
      throw std::runtime_error(e);
    }
    window->setCloseOnEmpty(true);
    m_lastShownColorFillWin = window;
  } else {
    if (NULL == window)
    {
      if (NULL == m_lastShownColorFillWin)
        return NULL;
      window = m_lastShownColorFillWin;
    }
    // start fresh layer
    window->setName(appWindow()->generateUniqueName( wsName + "-"));
    window->setLayersNumber(0);
    window->addLayer();
  }

  Graph *plot = window->activeGraph();
  appWindow()->setPreferences(plot);

  plot->setTitle(wsName);
  using MantidQt::API::PlotAxis;
  plot->setXAxisTitle(PlotAxis(*workspace, 0).title());
  plot->setYAxisTitle(PlotAxis(*workspace, 1).title());

  Spectrogram *spgrm = new Spectrogram(wsName, workspace);
  plot->plotSpectrogram(spgrm, curveType);
  connect(spgrm, SIGNAL(removeMe(Spectrogram*)),
          plot, SLOT(removeSpectrogram(Spectrogram*)));
  connect(plot, SIGNAL(curveRemoved()), window,
          SLOT(maybeNeedToClose()), Qt::QueuedConnection);

  appWindow()->setSpectrogramTickStyle(plot);
  plot->setAutoScale();

  QApplication::restoreOverrideCursor();
  return window;
}

/** Create a 1d graph form specified spectra in a MatrixWorkspace
@param wsName :: Workspace name
@param i0 :: Starting index
@param i1 :: Last index
@param errs :: If true include the errors to the graph
@param distr :: if true, workspace is a distribution
*/
MultiLayer* MantidUI::plotSpectraRange(const QString& wsName, int i0, int i1,
                                       MantidQt::DistributionFlag distr, bool errs)
{
  if (i0 < 0 || i1 < 0) return 0;
  /** For instrument with one to many spectra-detector mapping,
  * different pixels with correspond to the same specta so
  * we need to remove doublons in this case.
  */
  std::set<int> indexList;
  for(int i=i0;i<=i1;i++)
    indexList.insert(i);

  return plot1D(wsName,indexList,true, distr, errs);
}

/**  Create a graph and plot the selected rows of a MantidMatrix
@param m :: Mantid matrix
@param distr :: if true, workspace is a distribution
@param errs :: True if the errors to be plotted
*/
MultiLayer* MantidUI::plotSelectedRows(const MantidMatrix * const m,
                                       MantidQt::DistributionFlag distr,
                                       bool errs)
{
  const QList<int>& rows = m->getSelectedRows();
  std::set<int> rowSet(rows.constBegin(),rows.constEnd());

  return plot1D(m->workspaceName(),rowSet,true,distr, errs);
}

/**
 * Create a graph and plot the selected columns of a MantidMatrix
 * @param m MantidMatrix
 * @param errs True if errors are required
 * @return
 */
MultiLayer *MantidUI::plotSelectedColumns(const MantidMatrix * const m, bool errs)
{
  const QList<int>& cols = m->getSelectedColumns();
  std::set<int> colSet(cols.constBegin(),cols.constEnd());

  return plot1D(m->workspaceName(),colSet,false,MantidQt::DistributionFalse, errs);
}

Table* MantidUI::createTableFromBins(const QString& wsName, Mantid::API::MatrixWorkspace_const_sptr workspace,
                                     const QList<int>& bins, bool errs, int fromRow, int toRow)
{
  if (bins.empty()) return NULL;

  int c = errs?2:1;
  int numRows = static_cast<int>(workspace->getNumberHistograms());

  int j0 = fromRow >= 0? fromRow : 0;
  int j1 = toRow   >= 0? toRow   : numRows - 1;

  if (j0 >= numRows || j1 >= numRows) return NULL;

  Table* t = new Table(appWindow()->scriptingEnv(), numRows, c*bins.size() + 1, "", appWindow(), 0);
  appWindow()->initTable(t, appWindow()->generateUniqueName(wsName + "-"));

  for(int i = 0; i < bins.size(); i++)
  {
    const int kY = c*i+1;
    int kErr = 0;
    t->setColName(kY,"YB"+QString::number(bins[i]));
    if (errs)
    {
      kErr = 2*i + 2;
      t->setColPlotDesignation(kErr,Table::yErr);
      t->setColName(kErr,"EB"+QString::number(bins[i]));
    }
    for(int j = j0; j <= j1; j++)
    {
      const Mantid::MantidVec& dataY = workspace->readY(j);
      const Mantid::MantidVec& dataE = workspace->readE(j);

      if (i == 0)
      {
        // Get the X axis values from the vertical axis of the workspace
        if (workspace->axes() > 1) t->setCell(j,0,(*workspace->getAxis(1))(j));
        else t->setCell(j,0,j);
      }
      t->setCell(j,kY,dataY[bins[i]]);
      if (errs) t->setCell(j,kErr,dataE[bins[i]]);
    }
  }
  return t;
}

Table* MantidUI::createTableFromSelectedColumns(MantidMatrix *m, bool errs)
{
  const QList<int>& cols = m->getSelectedColumns();
  if (cols.empty()) return 0;

  int j0 = m->workspaceIndex(0);
  int j1 = m->workspaceIndex(m->numRows()-1);

  return createTableFromBins(m->name(), m->workspace(), cols, errs, j0, j1);

}

/** Saves data to  nexus file
* @param wsName :: Name of the workspace to be saved
* @param fileName :: name of the nexus file to created
*/
void MantidUI::savedatainNexusFormat(const std::string& fileName,const std::string & wsName)
{ 
  try
  {
    Mantid::API::IAlgorithm_sptr alg =createAlgorithm("SaveNexusProcessed");
    alg->setPropertyValue("Filename",fileName);
    alg->setPropertyValue("InputWorkspace",wsName);
    alg->execute();
  }
  catch(...)
  {
  }
}
/** Loads data from nexus file
* @param wsName :: Name of the workspace to be created
* @param fileName :: name of the nexus file
* @param project :: if true, load stops GUI execution
*/
void MantidUI::loaddataFromNexusFile(const std::string& wsName,const std::string& fileName,bool project)
{
  if(fileName.empty()) return ;
  try
  {
    Mantid::API::IAlgorithm_sptr alg =createAlgorithm("LoadNexus");
    alg->setPropertyValue("Filename",fileName);
    alg->setPropertyValue("OutputWorkspace",wsName);
    if(project)alg->execute();
    else executeAlgorithmAsync(alg);
  }
  catch(...)
  {
  }
}
/** Loads data from raw file
* @param wsName :: Name of the workspace to be created
* @param fileName :: name of the raw file
* @param project :: if true, load stops GUI execution
*/
void MantidUI::loadadataFromRawFile(const std::string& wsName,const std::string& fileName,bool project)
{
  if(fileName.empty()) return ;
  try
  {
    Mantid::API::IAlgorithm_sptr alg =createAlgorithm("LoadRaw");
    alg->setPropertyValue("Filename",fileName);
    alg->setPropertyValue("OutputWorkspace",wsName);
    if(project)alg->execute();
    else executeAlgorithmAsync(alg);
  }
  catch(...)
  {
  }
}
MantidMatrix* MantidUI::openMatrixWorkspace(ApplicationWindow* parent,const QString& wsName,int lower,int upper)
{
  (void) parent; //Avoid compiler warning

  MatrixWorkspace_sptr ws;
  if (AnalysisDataService::Instance().doesExist(wsName.toStdString()))
  {
    ws = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(wsName.toStdString());
  }

  if (!ws.get())return 0 ;

  MantidMatrix* w = new MantidMatrix(ws, appWindow(), "Mantid",wsName, lower, upper);
  if ( !w ) return 0;

  appWindow()->addMdiSubWindow(w);

  return w;
}

bool MantidUI::workspacesDockPlot1To1()
{
  return "On" == Mantid::Kernel::ConfigService::Instance().getString("MantidOptions.ReusePlotInstances");
}

//=========================================================================
//
// This section defines some stuff that is only used on Windows
//
//=========================================================================
#ifdef _WIN32

struct mem_block
{
  int size;
  int state;
};

///  Assess the virtual memeory of the current process.
void countVirtual(vector<mem_block>& mem, int& total)
{

  MEMORYSTATUSEX memStatus;
  memStatus.dwLength = sizeof(MEMORYSTATUSEX);
  GlobalMemoryStatusEx( &memStatus );

  MEMORY_BASIC_INFORMATION info;

  char *addr = 0;
  size_t free = 0;      // total free space
  size_t reserved = 0;  // total reserved space
  size_t committed = 0; // total commited (used) space
  size_t size = 0;
  size_t free_max = 0;     // maximum contiguous block of free memory
  size_t reserved_max = 0; // maximum contiguous block of reserved memory
  size_t committed_max = 0;// maximum contiguous block of committed memory

  size_t GB2 = memStatus.ullTotalVirtual;// Maximum memeory available to the process
  total = static_cast<int>(GB2);

  // Loop over all virtual memory to find out the status of every block.
  do
  {
    VirtualQuery(addr,&info,sizeof(MEMORY_BASIC_INFORMATION));

    int state = 0;
    if (info.State == MEM_FREE)
    {
      free += info.RegionSize;
      if (info.RegionSize > free_max) free_max = info.RegionSize;
      state = 0;
    }
    if (info.State == MEM_RESERVE)
    {
      reserved += info.RegionSize;
      if (info.RegionSize > reserved_max) reserved_max = info.RegionSize;
      state = 500;
    }
    if (info.State == MEM_COMMIT)
    {
      committed += info.RegionSize;
      if (info.RegionSize > committed_max) committed_max = info.RegionSize;
      state = 1000;
    }

    addr += info.RegionSize;
    size += info.RegionSize;

    mem_block b = {info.RegionSize, state};
    mem.push_back(b);

    /*cerr<<"BaseAddress = "<< info.BaseAddress<<'\n';
    cerr<<"AllocationBase = "<< info.AllocationBase<<'\n';
    cerr<<"AllocationProtect = "<< info.AllocationProtect<<'\n';
    cerr<<"RegionSize = "<< hex << info.RegionSize<<'\n';
    cerr<<"State = "<< state_str(info.State)<<'\n';
    cerr<<"Protect = "<< hex << info.Protect <<' '<< protect_str(info.Protect)<<'\n';
    cerr<<"Type = "<< hex << info.Type<<'\n';*/

  }
  while(size < GB2);


  std::cerr<<"count FREE = "<<std::dec<<double(free)/1024/1024<<'\n';
  std::cerr<<"count RESERVED = "<<double(reserved)/1024/1024<<'\n';
  std::cerr<<"count COMMITTED = "<<double(committed)/1024/1024<<'\n';

  std::cerr<<"max FREE = "<<std::dec<<double(free_max)/1024/1024<<'\n';
  std::cerr<<"max RESERVED = "<<double(reserved_max)/1024/1024<<'\n';
  std::cerr<<"max COMMITTED = "<<double(committed_max)/1024/1024<<'\n';
  std::cerr<<'\n';
}

/// Shows 2D plot of current memory usage.
/// One point is 1K of memory. One row is 1M.
/// Red - used memory block, blue - free, green - reserved.
void MantidUI::memoryImage()
{
  //ofstream ofil("memory.txt");
  vector<mem_block> mem;
  int total;
  countVirtual(mem,total);
  int colNum = 1024;
  int rowNum = total/1024/colNum;
  Matrix *m = appWindow()->newMatrix(rowNum,colNum);
  m->setCoordinates(0,colNum,0,rowNum);
  int row = 0;
  int col = 0;
  QImage image(colNum,rowNum,QImage::Format_Mono);
  for(vector<mem_block>::iterator b=mem.begin();b!=mem.end();++b)
  {
    int n = b->size/1024;
    for(int i=0;i<n;i++)
    {
      m->setCell(row,col,b->state);
      //ofil<<b->state<<'\t';
      col++;
      if (col >= colNum)
      {
        col = 0;
        row++;
        //ofil<<'\n';
      }
    }
  }
  appWindow()->plotSpectrogram(m, Graph::ColorMap);
}

void MantidUI::memoryImage2()
{
  //ofstream ofil("memory.txt");
  vector<mem_block> mem;
  int total;
  countVirtual(mem,total);
  int colNum = 1024;
  int rowNum = total/1024/colNum;
  int row = 0;
  int col = 0;
  QImage image(colNum,rowNum,QImage::Format_Mono);
  for(vector<mem_block>::iterator b=mem.begin();b!=mem.end();++b)
  {
    int n = b->size/1024;
    for(int i=0;i<n;i++)
    {
      if (row < rowNum && col < colNum)
      {
        image.setPixel(col,row,b->state > 600);
      }
      //ofil<<b->state<<'\t';
      col++;
      if (col >= colNum)
      {
        col = 0;
        row++;
        //ofil<<'\n';
      }
    }
  }
  image.save("memory_image.jpg");
}

#endif
//=======================================================================
// End of Windows specfic stuff
//=======================================================================

#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/CompAssembly.h"

void MantidUI::test()
{
  std::cerr<<"\nTest\n\n";

  MatrixWorkspace_const_sptr ws = boost::dynamic_pointer_cast<const MatrixWorkspace>(getSelectedWorkspace());
  if (ws)
  {
    boost::shared_ptr<const Mantid::Geometry::Instrument> instr = ws->getInstrument()->baseInstrument();
    boost::shared_ptr<Mantid::Geometry::CompAssembly> both = boost::dynamic_pointer_cast<Mantid::Geometry::CompAssembly>((*instr)[3]);
    if (both)
    {
      boost::shared_ptr<Mantid::Geometry::CompAssembly> first = boost::dynamic_pointer_cast<Mantid::Geometry::CompAssembly>((*both)[0]);
      if (first)
      {
        static int i = 0;
        Mantid::Kernel::V3D u = i++ ? Mantid::Kernel::V3D(1,0,0) : Mantid::Kernel::V3D(0,1,0);
        Mantid::Kernel::Quat q(30,u);
        first->rotate(q);
        return;
      }
    }
  }
  std::cerr<<"Failed...\n";
}