namespace OINA.Extender.Testharness
{
    using System;
    using System.Collections.Generic;
    using System.Collections.Specialized;
    using System.ComponentModel;
    using System.Drawing;
    using System.Drawing.Imaging;
    using System.Globalization;
    using System.IO;
    using System.Linq;
    using System.Runtime.Serialization;
    using System.Text;
    using System.Threading;
    using System.Windows.Forms;
    using OINA.Extender.Acquisition;
    using OINA.Extender.Acquisition.Ed;
    using OINA.Extender.Controls;
    using OINA.Extender.Controls.Common;
    using OINA.Extender.Controls.Image;
    using OINA.Extender.Controls.Spectrum;
    using OINA.Extender.Data;
    using OINA.Extender.Data.Ed;
    using OINA.Extender.Data.Image;
    using OINA.Extender.Processing;
    using OINA.Extender.Processing.Quant;
    using OINA.Extender.Testharness.Properties;
    using WindowsMedia = System.Windows.Media;

    /// <summary>
    /// MainForm Class
    /// </summary>
    public partial class MainForm : Form
    {
        /// <summary>
        /// List of EdSpectrum objects
        /// </summary>
        private readonly Dictionary<IEdSpectrum, AcquisitionItem> edSpectrumList = new Dictionary<IEdSpectrum, AcquisitionItem>();

        /// <summary>
        /// List of ElectronImage objects
        /// </summary>
        private readonly List<IElectronImage> electronImageList = new List<IElectronImage>();

        /// <summary>
        /// SpectrumViewer object
        /// </summary>
        private SpectrumViewer spectrumViewer;

        /// <summary>
        /// ElementCombo object for exclude element
        /// </summary>
        private ElementCombo excludeElementCombo;

        /// <summary>
        /// ElementCombo object for deconvolution element
        /// </summary>
        private ElementCombo deconvolutionElementCombo;

        /// <summary>
        /// The periodic table control
        /// </summary>
        private PeriodicTableControl periodicTableControl;

        /// <summary>
        /// imageViewer object
        /// </summary>
        private ImageViewer imageViewer;

        /// <summary>
        /// The comparison spectra
        /// </summary>
        private List<IEdSpectrum> comparisonSpectra;

        /// <summary>
        /// The periodic table control visual settings window
        /// </summary>
        private Form periodicTableVisualSettings;

        /// <summary>
        /// The element combo control visual settings window
        /// </summary>
        private Form elementComboVisualSettings;

        /// <summary>
        /// The spectrum viewer control visual settings window
        /// </summary>
        private Form spectrumViewerVisualSettings;

        /// <summary>
        /// The image viewer control visual settings window
        /// </summary>
        private Form imageViewVisualSettingsForm;

        /// <summary>
        /// The brightness/contrast dialog visual settings window
        /// </summary>
        private Form brightnessContrastDialogVisualSettings;

        /// <summary>
        /// The details dialog visual settings window
        /// </summary>
        private Form detailsDialogVisualSettingsForm;

        /// <summary>
        /// MainForm Constructor
        /// </summary>
        public MainForm()
        {
            this.InitializeComponent();

            this.LoadComparisonSpectra();

            this.cbCompareColor.DataSource = Enum.GetValues(typeof(KnownColor));
            this.imageToolComboBox.DataSource = Enum.GetValues(typeof(ImageInteractionTool));
            this.spectrumInteractionToolComboBox.DataSource = Enum.GetValues(typeof(InteractionTool));

            // Binding spectrum acquisition controller events
            OIHelper.EdSpectrumAcquisitionController.ExperimentStarted += this.OnEdSpectrumExperimentStarted;
            OIHelper.EdSpectrumAcquisitionController.ExperimentFinished += this.OnEdSpectrumExperimentFinished;

            // Binding image acquisition controller events
            OIHelper.ImageAcquisitionController.ExperimentStarted += this.OnImageExperimentStarted;
            OIHelper.ImageAcquisitionController.ExperimentFinished += this.OnImageExperimentFinished;

            // Initial UI contents
            this.InitialSpectrumViewerElementHost();
            this.InitialImageViewerElementHost();
            this.InitialPeriodicTableElementHost();
            this.InitialSpectrumSettingsContent();
            this.InitialImageSettingsContent();
            this.InitialTimers();
            this.InitialProcessingSettingsContent();
            this.InitializeEnabledElementsMenuItems();

            this.cbCompareColor.SelectedItem = GetRandomColor();
            this.spectrumInteractionToolComboBox.SelectedItem = this.spectrumViewer.InteractionTool;
            this.UpdateHighlightedElementInTable();
        }

        /// <summary>
        /// Gets the random color.
        /// </summary>
        /// <returns>A random color</returns>
        private static KnownColor GetRandomColor()
        {
            Random randomGen = new Random();

            KnownColor[] colors = Enum.GetValues(typeof(KnownColor)) as KnownColor[];

            int index = randomGen.Next(colors.Length);

            return colors[index];
        }

        /// <summary>
        /// Gets a value indicating whether this instance is acquiring.
        /// </summary>
        /// <value>
        /// <c>true</c> if this instance is acquiring; otherwise, <c>false</c>.
        /// </value>
        [System.Diagnostics.CodeAnalysis.SuppressMessage("Microsoft.Performance", "CA1822:MarkMembersAsStatic", Justification = "n/a")]
        private bool IsAcquiring
        {
            get { return OIHelper.EdSpectrumAcquisitionController.IsAcquiring; }
        }

        #region Status Event Handlers

        /// <summary>
        /// OnAcquisitionStatusTimerTicked
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EvenArgs</param>
        private void OnAcquisitionStatusTimerTicked(object sender, EventArgs e)
        {
            if (OIHelper.EdSpectrumAcquisitionController.IsAcquiring || OIHelper.ImageAcquisitionController.IsAcquiring)
            {
                this.lblAcquisitionStatus.Visible = !this.lblAcquisitionStatus.Visible;
            }
            else
            {
                this.lblAcquisitionStatus.Visible = false;
            }
        }

        /// <summary>
        /// OnIdentifyTimerTicked
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void OnIdentifyTimerTicked(object sender, EventArgs e)
        {
            this.DoAutoID();
        }

        /// <summary>
        /// Called when [ed spectrum experiment started].
        /// </summary>
        /// <param name="sender">The sender.</param>
        /// <param name="e">The <see cref="AcquisitionFinishedEventArgs{IEdSpectrum}"/> instance containing the event data.</param>
        private void OnEdSpectrumExperimentStarted(object sender, AcquisitionStartedEventArgs<IEdSpectrum> e)
        {
            var edSpectrum = e.Value;

            // execute on UI thread
            this.BeginInvoke((Action)delegate
            {
                this.spectrumViewer.Spectrum = edSpectrum;

                // Clear periodic table included and excluded elements
                this.periodicTableControl.ClearAll();

                // Update Known Elements
                this.periodicTableControl.IncludeElements(OIHelper.AutoIdSettings.KnownElements.ToArray());

                this.tmrIdentifyElements.Tick += this.OnIdentifyTimerTicked;
                this.tmrIdentifyElements.Enabled = true;
            });

            edSpectrum.PropertyChanged += this.OnPropertyChanged;
        }

        /// <summary>
        /// Called when [image experiment started].
        /// </summary>
        /// <param name="sender">The sender.</param>
        /// <param name="e">The instance containing the event data.</param>
        private void OnImageExperimentStarted(object sender, AcquisitionStartedEventArgs<IElectronImage[]> e)
        {
            // execute on UI thread
            this.BeginInvoke((Action)delegate
            {
                this.imageViewer.DisplayImage = e.Value[0];
            });
        }

        /// <summary>
        /// OnExperimentFinished
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">The instance containing the event data.</param>
        private void OnEdSpectrumExperimentFinished(object sender, AcquisitionFinishedEventArgs<IEdSpectrum> e)
        {
            e.Value.PropertyChanged -= this.OnPropertyChanged;

            this.tmrIdentifyElements.Tick -= this.OnIdentifyTimerTicked;
            this.tmrIdentifyElements.Enabled = false;

            // execute on UI thread
            this.BeginInvoke((Action)delegate
            {
                this.DoAutoID();
                this.UpdatePeriodicTable();
                this.DoQuant();

                if (this.edSpectrumList.ContainsKey(e.Value))
                {
                    this.AcquisitionQueueListBox.Items.Remove(this.edSpectrumList[e.Value]);
                    this.edSpectrumList.Remove(e.Value);
                }

                // *** If this is the last experiment, call EndMultipleAcquisition on the Acquisition 
                // *** controller, to re-enable external scan switching
                if (!this.edSpectrumList.Any())
                {
                    OIHelper.EdSpectrumAcquisitionController.EndMultipleAcquisition();
                }
            });
        }

        /// <summary>
        /// Called when [image experiment finished].
        /// </summary>
        /// <param name="sender">The sender.</param>
        /// <param name="e">The instance containing the event data.</param>
        private void OnImageExperimentFinished(object sender, AcquisitionFinishedEventArgs<IElectronImage[]> e)
        {
            // execute on UI thread
            this.BeginInvoke((Action)delegate
            {
                e.Value.ToList().ForEach(i =>
                    {
                        this.electronImageList.Remove(i);
                        this.ImageAcquisitionQueueListBox.Items.Remove(i);
                    });
            });
        }

        /// <summary>
        /// OnPropertyChanged
        /// </summary>
        /// <param name="sender">Event source</param>
        /// <param name="e">Event arguments</param>
        private void OnPropertyChanged(object sender, PropertyChangedEventArgs e)
        {
            var edSpectrum = sender as IEdSpectrum;

            switch (e.PropertyName)
            {
                case "RealTimeSeconds":
                    this.Invoke((MethodInvoker)delegate
                    {
                        this.textRealTimeSeconds.Text = edSpectrum.RealTimeSeconds.ToString(@"0.000", CultureInfo.InvariantCulture);
                    });
                    break;
                case "LiveTimeSeconds":
                    this.Invoke((MethodInvoker)delegate
                    {
                        this.textLiveTimeSeconds.Text = edSpectrum.LiveTimeSeconds.ToString(@"0.000", CultureInfo.InvariantCulture);
                    });
                    break;
                case "OutputRate":
                    this.Invoke((MethodInvoker)delegate
                    {
                        this.outputStatus.Text = OIHelper.MonitoringController.EdStatus.Values.Sum(status => status.OutputRate).ToString(CultureInfo.InvariantCulture) + @"cps";
                    });
                    break;
                case "DeadTime":
                    this.Invoke((MethodInvoker)delegate
                    {
                        this.deadtimeStatus.Text = OIHelper.MonitoringController.EdStatus.Values.Max(status => status.DeadTime).ToString(CultureInfo.InvariantCulture) + @"%";
                    });
                    break;
            }
        }

        #endregion

        #region Update UI status

        /// <summary>
        /// InitialSpectrumSettingsContent
        /// </summary>
        private void InitialSpectrumSettingsContent()
        {
            if (OIHelper.EdSpectrumSettings.EdCapabilities.HasHardwareConnection)
            {
                this.textSpectrumLabel.Text = @"Spectrum 1";

                this.cbAcquisitionMode.Items.Add(EdAcquireMode.LiveTime);
                this.cbAcquisitionMode.Items.Add(EdAcquireMode.RealTime);
                this.cbAcquisitionMode.SelectedIndex = 0;

                this.AcquisitionTimeNumericUpDown.Value = 10;

                this.cbProcessTime.DataSource = OIHelper.EdSpectrumSettings.EdCapabilities.AllowedProcessTimes;
                this.cbProcessTime.SelectedIndex = 3;

                this.cbEnergyRange.DataSource = OIHelper.EdSpectrumSettings.EdCapabilities.AllowedEnergyRanges;
                this.cbEnergyRange.SelectedIndex = 1;

                this.cbChannelNumber.DataSource = OIHelper.EdSpectrumSettings.EdCapabilities.AllowedNumberOfChannels;
                this.cbChannelNumber.SelectedIndex = 1;
            }
        }

        /// <summary>
        /// InitialImageSettingsContent
        /// </summary>
        private void InitialImageSettingsContent()
        {
            var settings = OIHelper.ImageSettings;

            if (settings.ImageCapabilities.HasHardwareConnection)
            {
                this.cbImageScanSize.DataSource = OIHelper.GetScanSizes(
                    settings.ScanCapabilities.MinimumPixelSize,
                    settings.ScanCapabilities.MaximumPixelSize);

                this.cbImageScanSize.SelectedIndex = this.cbImageScanSize.Items.Count > 4 ? 4 : this.cbImageScanSize.Items.Count - 1;

                this.cbInputSignal.DataSource = settings.ImageCapabilities.AllowedInputSources;
                this.cbInputSignal.SelectedIndex = 0;
                this.tbNumberOfFrames.Text = @"1";
                this.tbDwellTime.Text = @"40";
            }
        }

        /// <summary>
        /// Initial Timers
        /// </summary>
        private void InitialTimers()
        {
            this.tmrAcquisitionStatus.Enabled = true;
            this.tmrAcquisitionStatus.Interval = 1000;
            this.tmrAcquisitionStatus.Tick += this.OnAcquisitionStatusTimerTicked;

            this.tmrIdentifyElements.Enabled = false;
            this.tmrIdentifyElements.Interval = 1000;
        }

        /// <summary>
        /// InitialProcessingSettingsContent
        /// </summary>
        private void InitialProcessingSettingsContent()
        {
            this.rbAllElements.Checked = true;

            this.tbCombinedElement.Enabled = false;
            this.tbCombinedElement.Text = @"8";

            this.tbNumberOfIons.Enabled = false;
            this.tbNumberOfIons.Text = @"3.0";

            this.deconvolutionElementCombo = new ElementCombo();
            this.ehDeconvolutionElement.Child = this.deconvolutionElementCombo;
            this.deconvolutionElementCombo.DisplayFormat = ElementComboDisplayFormat.ShowSymbol;
            foreach (int i in OIHelper.SEMQuantSettings.DeconvolutionElements)
            {
                this.tbDeconvolutionElementList.Text += i.ToString(CultureInfo.InvariantCulture) + System.Environment.NewLine;
            }

            this.cbThresholding.Checked = false;
            this.tbSigmaLevel.Enabled = false;
            this.tbSigmaLevel.Text = @"3.0";

            this.cbIsCoated.Checked = OIHelper.SEMQuantSettings.SampleCoating.IsCoated;
            this.tbCoatingElement.Enabled = OIHelper.SEMQuantSettings.SampleCoating.IsCoated;
            this.tbCoatingElement.Text = OIHelper.SEMQuantSettings.SampleCoating.CoatingElement.ToString(CultureInfo.InvariantCulture);
            this.tbDensity.Enabled = OIHelper.SEMQuantSettings.SampleCoating.IsCoated;
            this.tbDensity.Text = OIHelper.SEMQuantSettings.SampleCoating.Density.ToString(CultureInfo.InvariantCulture);
            this.tbThickness.Enabled = OIHelper.SEMQuantSettings.SampleCoating.IsCoated;
            this.tbThickness.Text = OIHelper.SEMQuantSettings.SampleCoating.Thickness.ToString(CultureInfo.InvariantCulture);

            this.excludeElementCombo = new ElementCombo();
            this.ehExcludeElement.Child = this.excludeElementCombo;
            this.excludeElementCombo.DisplayFormat = ElementComboDisplayFormat.ShowName;
            this.excludeElementCombo.PropertyChanged += this.ExcludeElementCombo_PropertyChanged;
            this.UpdateElementsList(this.periodicTableControl.ExcludedElements, this.tbExcludedElementList);
            this.UpdateElementsList(this.periodicTableControl.IncludedElements, this.tbIncludedElementList);
            this.UpdateElementsList(this.periodicTableControl.UnsetElements, this.tbUnsetElementList);
        }

        /// <summary>
        /// InitialSpectrumViewerElementHost
        /// </summary>
        private void InitialSpectrumViewerElementHost()
        {
            this.spectrumViewer = new SpectrumViewer();
            this.ehSpectrumViewer.Child = this.spectrumViewer;
            this.spectrumViewer.IsXAxisAutoScaleEnabled = false;
            this.spectrumViewer.IsYAxisAutoScaleEnabled = true;
        }

        /// <summary>
        /// InitialImageViewerElementHost
        /// </summary>
        private void InitialImageViewerElementHost()
        {
            this.imageViewer = new ImageViewer();
            this.ehImageViewer.Child = this.imageViewer;
        }

        /// <summary>
        /// Initials the periodic table element host.
        /// </summary>
        private void InitialPeriodicTableElementHost()
        {
            this.periodicTableControl = new PeriodicTableControl();
            this.periodicTableElementHost.Child = this.periodicTableControl;

            // Set the Periodic Table BackColor (0xFF07366B) same as Spectrum Viewer 
            this.periodicTableElementHost.BackColor = Color.FromArgb(255, 7, 54, 107);

            foreach (object knownColor in Enum.GetValues(typeof(System.Drawing.KnownColor)))
            {
                this.periodicTableBackgroundToolStripComboBox.Items.Add(knownColor);
            }

            ((INotifyCollectionChanged)this.periodicTableControl.ExcludedElements).CollectionChanged += this.PeriodicTableExcludedElements_CollectionChanged;
            ((INotifyCollectionChanged)this.periodicTableControl.IncludedElements).CollectionChanged += this.PeriodicTableIncludedElements_CollectionChanged;
            ((INotifyCollectionChanged)this.periodicTableControl.UnsetElements).CollectionChanged += this.PeriodicTableUnsetElements_CollectionChanged;
        }

        /// <summary>
        /// Update the Periodic Table content after acquisition finished
        /// </summary>
        private void UpdatePeriodicTable()
        {
            this.periodicTableControl.IncludeElements(this.spectrumViewer.Spectrum.IdentifiedElements.ToArray());
        }

        /// <summary>
        /// Updates the elements list.
        /// </summary>
        /// <param name="data">The data.</param>
        /// <param name="list">The list.</param>
        [System.Diagnostics.CodeAnalysis.SuppressMessage("Microsoft.Performance", "CA1822:MarkMembersAsStatic", Justification = "Ignore")]
        private void UpdateElementsList(IEnumerable<int> data, TextBox list)
        {
            list.Clear();

            foreach (int i in data.OrderBy(x => x).ToArray<int>())
            {
                list.Text += ElementProperties.GetElementName(i) + System.Environment.NewLine;
            }
        }

        #endregion

        #region Control acquisition from UI

        /// <summary>
        /// StartAcquisition button click handler
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void StartAcquisitionButton_Click(object sender, EventArgs e)
        {
            this.spectrumViewer.ClearComparisonSpectra();

            this.AcquireSpectrum(false);
        }

        /// <summary>
        /// ResumeAcquisition button click handler
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void ResumeAcquisitionButton_Click(object sender, EventArgs e)
        {
            if (this.spectrumViewer.Spectrum != null && !this.IsAcquiring)
            {
                this.AcquireSpectrum(true);
            }
        }

        /// <summary>
        /// Start Acquire Spectrum Process
        /// </summary>
        /// <param name="isResume">true if is resume</param>
        private void AcquireSpectrum(bool isResume)
        {
            IEdSpectrum edSpectrum = null;

            // Spectrum acquisition settings confirm
            var edSpectrumSettings = OIHelper.EdSpectrumSettings;
            var edSpectrumAcquisitionController = OIHelper.EdSpectrumAcquisitionController;

            edSpectrumSettings.EdSettings.AcquisitionMode = (EdAcquireMode)this.cbAcquisitionMode.SelectedItem;
            edSpectrumSettings.EdSettings.AcquisitionTime = TimeSpan.FromSeconds((int)this.AcquisitionTimeNumericUpDown.Value);
            edSpectrumSettings.EdSettings.ProcessTime = (int)this.cbProcessTime.SelectedValue;
            edSpectrumSettings.EdSettings.EnergyRange = (int)this.cbEnergyRange.SelectedValue;
            edSpectrumSettings.EdSettings.NumberOfChannels = (int)this.cbChannelNumber.SelectedValue;
            edSpectrumSettings.ScanSettings.AcquisitionRegion.CreateMicroscopeRegion();

            // SpectrumViewer settings confirm
            this.spectrumViewer.MaximumEnergy = edSpectrumSettings.EdSettings.EnergyRange;

            // If Ed hardware is not ready, the software will crash. 
            if (edSpectrumAcquisitionController.IsEdHardwareReady(edSpectrumSettings))
            {
                // *** If this is the first acquisition, call BeginMultipleAcquisition 
                // *** on the AcquisitionController to suppress external scan switching
                if (!this.edSpectrumList.Any())
                {
                    edSpectrumAcquisitionController.BeginMultipleAcquisition();
                }

                if (!isResume)
                {
                    // Start spectrum acquisition
                    try
                    {
                        edSpectrum = edSpectrumAcquisitionController.StartAcquisition(edSpectrumSettings);
                        edSpectrum.Label = string.Format(CultureInfo.CurrentCulture, @"{0} ({1:HH:mm:ss})", this.textSpectrumLabel.Text, DateTime.Now);

                        this.edSpectrumList.Add(edSpectrum, new AcquisitionItem(edSpectrum, OIHelper.EdSpectrumSettings.EdSettings.AcquisitionMode, OIHelper.EdSpectrumSettings.EdSettings.AcquisitionTime.TotalMilliseconds, this.AcquisitionQueueListBox));
                        this.AcquisitionQueueListBox.Items.Add(this.edSpectrumList[edSpectrum]);
                    }
                    catch (InvalidSettingsException invalidSettingsException)
                    {
                        MessageBox.Show(invalidSettingsException.Message, Resources.CannotStartAcquisitionTitle, MessageBoxButtons.OK, MessageBoxIcon.Exclamation, MessageBoxDefaultButton.Button1, MessageBoxOptions.DefaultDesktopOnly);
                    }
                    catch (AcquisitionStartException acquisitionStartException)
                    {
                        MessageBox.Show(acquisitionStartException.Message, Resources.CannotStartAcquisitionTitle, MessageBoxButtons.OK, MessageBoxIcon.Exclamation, MessageBoxDefaultButton.Button1, MessageBoxOptions.DefaultDesktopOnly);
                    }
                }
                else
                {
                    edSpectrum = this.spectrumViewer.Spectrum;
                    edSpectrumAcquisitionController.ResumeAcquisition(edSpectrumSettings, edSpectrum);
                    this.edSpectrumList.Add(edSpectrum, new AcquisitionItem(edSpectrum, OIHelper.EdSpectrumSettings.EdSettings.AcquisitionMode, OIHelper.EdSpectrumSettings.EdSettings.AcquisitionTime.TotalMilliseconds, this.AcquisitionQueueListBox));
                    this.AcquisitionQueueListBox.Items.Add(this.edSpectrumList[edSpectrum]);
                }
            }
        }

        /// <summary>
        /// StopAcquisition button click handler
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void StopAcquisitionButton_Click(object sender, EventArgs e)
        {
            if (OIHelper.EdSpectrumAcquisitionController.IsAcquiring == true)
            {
                OIHelper.EdSpectrumAcquisitionController.StopAcquisition();
            }
        }

        /// <summary>
        /// Handles the Click event of Calculate button.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void CalculateButton_Click(object sender, EventArgs e)
        {
            try
            {
                int atomicNum = ElementProperties.GetAtomicNumberByElementSymbol(this.tbIdentifiedElement.SelectedText);

                var peakParameters = OIHelper.EdSpectrumProcessing.CalculatePeakParameters(this.spectrumViewer.Spectrum, atomicNum);
                this.tbEnergy.Text = peakParameters.Centre.ToString(CultureInfo.InvariantCulture);
                this.tbFWHM.Text = peakParameters.FWHM.ToString(CultureInfo.InvariantCulture);
            }
            catch (NullReferenceException)
            {
            }
            catch (FormatException)
            {
            }
            catch (InvalidOperationException)
            {
            }
        }

        /// <summary>
        /// Handles the Click event of StartImageScan button.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void StartImageScanButton_Click(object sender, EventArgs e)
        {
            var imageSettings = OIHelper.ImageSettings.ImageSettings;
            var imageCapabilities = OIHelper.ImageSettings.ImageCapabilities;
            var scanSettings = OIHelper.ImageSettings.ScanSettings;
            var imageAcquisitionController = OIHelper.ImageAcquisitionController;

            this.tbImageData.Text = string.Empty;
            this.tbPointX.Text = string.Empty;
            this.tbPointY.Text = string.Empty;

            var value = int.Parse(this.tbDwellTime.Text, CultureInfo.InvariantCulture);

            if (value > imageCapabilities.MaximumImageDwellMicroseconds)
            {
                imageSettings.DwellTimeMicroSeconds = imageCapabilities.MaximumImageDwellMicroseconds;
            }

            if (value < imageCapabilities.MinimumImageDwellMicroseconds)
            {
                imageSettings.DwellTimeMicroSeconds = imageCapabilities.MinimumImageDwellMicroseconds;
            }
            else
            {
                imageSettings.DwellTimeMicroSeconds = value;
            }

            // *** Disable all input sources before enabling the one that the user has chosen
            imageSettings.InputSources.ToList().ForEach(i => imageSettings.EnableInputSource(i.Key, false));
            imageSettings.EnableInputSource((ImageInputSources)this.cbInputSignal.SelectedItem, true);

            scanSettings.FrameCount = int.Parse(this.tbNumberOfFrames.Text, CultureInfo.InvariantCulture);

            var pixelSize = 1d / double.Parse(this.cbImageScanSize.Text, CultureInfo.InvariantCulture);

            scanSettings.AcquisitionRegion.CreateFullFieldRegion(pixelSize);

            try
            {
                var images = imageAcquisitionController.StartAcquisition(OIHelper.ImageSettings).ToList();
                images.ForEach(i =>
                    {
                        i.Label = string.Format(CultureInfo.CurrentCulture, @"{0} ({1:HH:mm:ss})", @"ElectronImage", DateTime.Now);

                        this.electronImageList.Add(i);
                        this.ImageAcquisitionQueueListBox.Items.Add(i);
                    });
            }
            catch (InvalidSettingsException exception)
            {
                var sb = new StringBuilder(@"Invalid settings have been supplied:");
                sb.AppendLine();
                exception.ValidationResults.ValidationErrors
                    .ToList()
                    .ForEach(ve => sb.AppendFormat(CultureInfo.CurrentCulture, @"{0}      {1}", Environment.NewLine, ve));

                MessageBox.Show(sb.ToString(), @"Invalid settings", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
            }
        }

        /// <summary>
        /// Handles the Click event of StopImageScan button.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void StopImageScanButton_Click(object sender, EventArgs e)
        {
            if (OIHelper.ImageAcquisitionController.IsAcquiring)
            {
                OIHelper.ImageAcquisitionController.StopAcquisition();
            }
        }

        /// <summary>
        /// Handles the Click event of GetPixelData button.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void GetPixelDataButton_Click(object sender, EventArgs e)
        {
            if ((!OIHelper.ImageAcquisitionController.IsAcquiring) & (this.imageViewer.DisplayImage != null))
            {
                var electronImage = this.imageViewer.DisplayImage as IElectronImage;
                if (electronImage != null)
                {
                    try
                    {
                        int x = int.Parse(this.tbPointX.Text, CultureInfo.InvariantCulture);
                        int y = int.Parse(this.tbPointY.Text, CultureInfo.InvariantCulture);

                        var stringBuilder = new StringBuilder();
                        stringBuilder.AppendFormat(CultureInfo.CurrentCulture, @" Point({0},{1}), Value: {2}", x, y, electronImage.GetData(new Point(x, y)));
                        stringBuilder.Append(Environment.NewLine);
                        this.tbImageData.Text = stringBuilder.ToString();
                    }
                    catch (ArgumentOutOfRangeException)
                    {
                        //// stringBuilder - The length of the expanded string would exceed MaxCapacity.
                    }
                    catch (FormatException)
                    {
                        //// int.Parse - The x or y coordinates are not in the correct format.
                    }
                }
            }
        }

        #endregion

        #region ToolStripMenuItem handlers

        /// <summary>
        /// Handles the Click event of the elementComboVisualSettingsToolStripMenuItem control.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">instance containing the event data.</param>
        private void ExportSpectrumAsToolStripMenuItem_Click(object sender, EventArgs e)
        {
            string filter = @"Bitmap (*.bmp)|*.bmp|PNG (*.png)|*.png|TIFF (*.tif)|*.tif|JPEG (*.jpg)|*.jpg";
            string title = @"Export Spectrum As...";
            try
            {
                short width = (short)this.spectrumViewer.ActualWidth;
                short height = (short)this.spectrumViewer.ActualHeight;
                Bitmap bitmap = OIHelper.EdSpectrumProcessing.CreateBitmap(this.spectrumViewer.Spectrum, width, height);
                using (SaveFileDialog exportSpectrumDialog = new SaveFileDialog())
                {
                    exportSpectrumDialog.Filter = filter;
                    exportSpectrumDialog.Title = title;
                    exportSpectrumDialog.FilterIndex = 1;
                    if (exportSpectrumDialog.ShowDialog() == DialogResult.OK)
                    {
                        switch (exportSpectrumDialog.FilterIndex)
                        {
                            case 1:
                                bitmap.Save(exportSpectrumDialog.FileName, ImageFormat.Bmp);
                                break;
                            case 2:
                                bitmap.Save(exportSpectrumDialog.FileName, ImageFormat.Png);
                                break;
                            case 3:
                                bitmap.Save(exportSpectrumDialog.FileName, ImageFormat.Tiff);
                                break;
                            case 4:
                                bitmap.Save(exportSpectrumDialog.FileName, ImageFormat.Jpeg);
                                break;
                            default:
                                bitmap.Save(exportSpectrumDialog.FileName, ImageFormat.Bmp);
                                break;
                        }
                    }
                }
            }
            catch (ArgumentException)
            {
            }
        }

        /// <summary>
        /// ExitToolStripMenuItem click handler
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void ExitToolStripMenuItem_Click(object sender, EventArgs e)
        {
            Application.Exit();
        }

        /// <summary>
        /// Detector Control Tool strip menu item click handler
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void DetectorControlToolStripMenuItem_Click(object sender, EventArgs e)
        {
            Form detectorControlPanel = new DetectorControlPanel(OIHelper.EdDetectorControl);
            detectorControlPanel.Show();
        }

        /// <summary>
        /// Microscope Control Tool strip menu item click handler
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void MicroscopeControlToolStripMenuItem_Click(object sender, EventArgs e)
        {
            Form microscopeControlPanel = new MicroscopeControlPanel();
            microscopeControlPanel.Show();
        }

        /// <summary>
        /// Calibrate ToolStrip MenuItem Click event handler.
        /// </summary>
        /// <param name="sender">sender</param>
        /// <param name="e">e</param>
        private void CalibrateToolStripMenuItem_Click(object sender, EventArgs e)
        {
            Form calibrate = new Calibrate();
            calibrate.Show();
        }

        /// <summary>
        /// Auto Id Settings Form
        /// </summary>
        /// <param name="sender">sender</param>
        /// <param name="e">EventArgs</param>
        private void AutoIdSettingsToolStripMenuItem_Click(object sender, EventArgs e)
        {
            Form autoIDSettings = new AutoIdSettings();
            autoIDSettings.Show();
        }

        /// <summary>
        /// Handles the Click event of the periodicTableVisualSettingsToolStripMenuItem control.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void PeriodicTableVisualSettingsToolStripMenuItem_Click(object sender, EventArgs e)
        {
            if (this.periodicTableVisualSettings == null || this.periodicTableVisualSettings.IsDisposed)
            {
                this.periodicTableVisualSettings = new PeriodicTableVisualSettings();
            }

            this.periodicTableVisualSettings.Show();
            this.periodicTableVisualSettings.BringToFront();
        }

        /// <summary>
        /// Handles the Click event of the elementComboVisualSettingsToolStripMenuItem control.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void ElementComboVisualSettingsToolStripMenuItem_Click(object sender, EventArgs e)
        {
            if (this.elementComboVisualSettings == null || this.elementComboVisualSettings.IsDisposed)
            {
                this.elementComboVisualSettings = new ElementComboVisualSettings();
            }

            this.elementComboVisualSettings.Show();
            this.elementComboVisualSettings.BringToFront();
        }

        /// <summary>
        /// Handles the Click event of the SpectrumViewerVisualSettingsToolStripMenuItem control.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void SpectrumViewerVisualSettingsToolStripMenuItem_Click(object sender, EventArgs e)
        {
            if (this.spectrumViewerVisualSettings == null || this.spectrumViewerVisualSettings.IsDisposed)
            {
                this.spectrumViewerVisualSettings = new SpectrumViewerVisualSettings();
            }

            this.spectrumViewerVisualSettings.Show();
            this.spectrumViewerVisualSettings.BringToFront();
        }

        /// <summary>
        /// Handles the Click event of the ImageViewerVisualSetting control.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void ImageViewerVisualSetting_Click(object sender, EventArgs e)
        {
            if (this.imageViewVisualSettingsForm == null || this.imageViewVisualSettingsForm.IsDisposed)
            {
                this.imageViewVisualSettingsForm = new ImageViewerVisualSettings();
            }

            this.imageViewVisualSettingsForm.Show();
            this.imageViewVisualSettingsForm.BringToFront();
        }

        /// <summary>
        /// Handles the Click event of the BrightnessContractDialogVisualSettingsToolStripMenuItem control.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void BrightnessContractDialogVisualSettingsToolStripMenuItem_Click(object sender, EventArgs e)
        {
            if (this.brightnessContrastDialogVisualSettings == null || this.brightnessContrastDialogVisualSettings.IsDisposed)
            {
                this.brightnessContrastDialogVisualSettings = new BCDialogVisualSettings();
            }

            this.brightnessContrastDialogVisualSettings.Show();
            this.brightnessContrastDialogVisualSettings.BringToFront();
        }

        /// <summary>
        /// Called when [details visual settings menu item click].
        /// </summary>
        /// <param name="sender">The sender.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void OnDetailsVisualSettingsMenuItemClick(object sender, EventArgs e)
        {
            if (this.detailsDialogVisualSettingsForm == null || this.detailsDialogVisualSettingsForm.IsDisposed)
            {
                this.detailsDialogVisualSettingsForm = new DetailDialogVisualSettings();
            }

            this.detailsDialogVisualSettingsForm.Show();
            this.detailsDialogVisualSettingsForm.BringToFront();
        }

        /// <summary>
        /// Handles the Click event of the LoadSpectrumDataToolStripMenuItem_Click.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void LoadSpectrumDataToolStripMenuItem_Click(object sender, EventArgs e)
        {
            try
            {
                using (var of_dlg = new OpenFileDialog())
                {
                    of_dlg.Title = @"Select a file";
                    of_dlg.Filter = @"Esd(*.esd)|*.esd|Iex(*.iex)|*.iex";

                    of_dlg.FilterIndex = 1;
                    if (of_dlg.ShowDialog() == DialogResult.OK)
                    {
                        if (!File.Exists(of_dlg.FileName))
                        {
                            throw new InvalidOperationException("File does not exists!");
                        }

                        this.spectrumViewer.ClearComparisonSpectra();
                        switch (of_dlg.FilterIndex)
                        {
                            case 1:
                                this.spectrumViewer.Spectrum = DataFactory.LoadEdSpectrum(OIHelper.FileToByteArray(of_dlg.FileName));
                                break;
                            case 2:
                                this.spectrumViewer.Spectrum = DataFactory.LoadEdSpectrumFromIex(of_dlg.FileName);
                                break;
                        }

                        // Set Periodic Table control element state
                        this.periodicTableControl.ClearAll();
                        this.periodicTableControl.IncludeElements(this.spectrumViewer.Spectrum.IdentifiedElements.ToArray());
                    }
                }
            }
            catch (SerializationException)
            {
            }
        }

        /// <summary>
        /// SaveSpectrumDataToolStripMenuItem_Click
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void SaveSpectrumDataToolStripMenuItem_Click(object sender, EventArgs e)
        {
            string filter = @"Esd(*.esd)|*.esd|Iex(*.iex)|*.iex";
            string title = @"Save spectrum as";

            var spectrum = this.spectrumViewer.Spectrum;
            if (spectrum != null)
            {
                try
                {
                    using (var dialog = new SaveFileDialog())
                    {
                        dialog.Filter = filter;
                        dialog.Title = title;
                        dialog.FilterIndex = 1;
                        if (dialog.ShowDialog() == DialogResult.OK)
                        {
                            switch (dialog.FilterIndex)
                            {
                                case 1:
                                    byte[] spectrumData = spectrum.Save();
                                    OIHelper.ByteArrayToFile(dialog.FileName, spectrumData);
                                    break;
                                case 2:
                                    OIHelper.EdSpectrumProcessing.CreateIexSpectrum(dialog.FileName, spectrum);
                                    break;
                                default:
                                    break;
                            }
                        }
                    }
                }
                catch (ArgumentException)
                {
                }
            }
        }

        /// <summary>
        /// Handles the Click event of the LoadImageDataToolStripMenuItem_Click.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void LoadImageDataToolStripMenuItem_Click(object sender, EventArgs e)
        {
            try
            {
                using (OpenFileDialog dialog = new OpenFileDialog())
                {
                    dialog.Title = @"Select a file";
                    dialog.Filter = @"Img(*.img)|*.img";

                    dialog.FilterIndex = 1;
                    if (dialog.ShowDialog() == DialogResult.OK)
                    {
                        this.imageViewer.DisplayImage = null;
                        if (!File.Exists(dialog.FileName))
                        {
                            throw new System.InvalidOperationException("File does not exists!");
                        }

                        this.imageViewer.DisplayImage = DataFactory.LoadElectronImage(OIHelper.FileToByteArray(dialog.FileName));
                    }
                }
            }
            catch (SerializationException)
            {
            }
        }

        /// <summary>
        /// SaveImageDataToolStripMenuItem_Click
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void SaveImageDataToolStripMenuItem_Click(object sender, EventArgs e)
        {
            string filter = @"Img(*.img)|*.img";
            string title = @"Save image as";
            if (this.imageViewer.DisplayImage != null)
            {
                try
                {
                    var electronImage = this.imageViewer.DisplayImage;
                    using (SaveFileDialog dialog = new SaveFileDialog())
                    {
                        dialog.Filter = filter;
                        dialog.Title = title;
                        dialog.FilterIndex = 1;
                        if (dialog.ShowDialog() == DialogResult.OK)
                        {
                            byte[] imageData = electronImage.Save();
                            OIHelper.ByteArrayToFile(dialog.FileName, imageData);
                        }
                    }
                }
                catch (ArgumentException)
                {
                }
            }
        }

        /// <summary>
        /// EDMapAcquisitionToolStripMenuItem_Click
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">instance containing the event data.</param>
        private void EDMapAcquisitionToolStripMenuItem_Click(object sender, EventArgs e)
        {
#if ENABLE_MAP_ACQUIRE
            EdMapAcquisition edMapAcquisition = new EdMapAcquisition();
            edMapAcquisition.Show();
#endif
        }

        #endregion

        #region Control Spectrum Processing

        #region Control AutoID

        /// <summary>
        /// Add element to excluded list
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void AddExcludeButton_Click(object sender, EventArgs e)
        {
            int element = this.excludeElementCombo.CurrentElement;
            try
            {
                this.periodicTableControl.ExcludeElements(element);
            }
            catch (FormatException fe)
            {
                this.tbExcludedElementList.Text = fe.Message;
            }
        }

        /// <summary>
        /// Remove element from excluded list
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void DeleteExcludeButton_Click(object sender, EventArgs e)
        {
            int element = this.excludeElementCombo.CurrentElement;

            try
            {
                this.periodicTableControl.Clear(element);
            }
            catch (FormatException fe)
            {
                this.tbExcludedElementList.Text = fe.Message;
            }
        }

        /// <summary>
        /// Do AutoID Button Click Handler
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void DoAutoIDButton_Click(object sender, EventArgs e)
        {
            this.DoAutoID();
        }

        /// <summary>
        /// Do AutoID
        /// </summary>
        private void DoAutoID()
        {
            var spectrum = this.spectrumViewer.Spectrum;
            if (spectrum != null)
            {
                this.tbIdentifiedElement.Clear();
                IEnumerable<int> elementList = OIHelper.EdSpectrumProcessing.IdentifyElements(
                    spectrum,
                    OIHelper.AutoIdSettings);

                foreach (int i in elementList)
                {
                    this.tbIdentifiedElement.Text = this.tbIdentifiedElement.Text +
                                                    ElementProperties.GetElementSymbol(i) +
                                                    Environment.NewLine;
                }

                // Update spectrum peak label
                this.UpdateSpectrumPeakLabels();
            }
        }

        /// <summary>
        /// Update current spectrum peak labels
        /// </summary>
        private void UpdateSpectrumPeakLabels()
        {
            try
            {
                OIHelper.EdSpectrumProcessing.UpdatePeakLabels(this.spectrumViewer.Spectrum, null);
            }
            catch (ArgumentNullException)
            {
            }
            catch (InvalidOperationException)
            {
            }
        }

        #endregion

        #region Control Quantitative Analysis

        /// <summary>
        /// Do quant button click handler
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void DoQuantButton_Click(object sender, EventArgs e)
        {
            this.DoQuant();
        }

        /// <summary>
        /// Do quantitative processing and display
        /// </summary>
        private void DoQuant()
        {
            switch (OIHelper.SEMQuantSettings.ProcessingOption)
            {
                case ProcessingOption.ElementByDifference:
                    OIHelper.SEMQuantSettings.CombinedElement = int.Parse(this.tbCombinedElement.Text, CultureInfo.InvariantCulture);
                    break;
                case ProcessingOption.ElementByStoichiometry:
                    // While it is possible to choose other elements, Oxygen is the only supported element by stoichiometry.
                    OIHelper.SEMQuantSettings.CombinedElement = 8;
                    OIHelper.SEMQuantSettings.TypeOfIon = IonType.Anion;
                    OIHelper.SEMQuantSettings.NumberOfIons = double.Parse(this.tbNumberOfIons.Text, CultureInfo.InvariantCulture);
                    break;
                case ProcessingOption.AllElements:
                default:
                    break;
            }

            if (this.cbIsCoated.Checked)
            {
                OIHelper.SEMQuantSettings.SampleCoating.IsCoated = true;
                OIHelper.SEMQuantSettings.SampleCoating.Thickness = double.Parse(this.tbThickness.Text, CultureInfo.InvariantCulture);
                OIHelper.SEMQuantSettings.SampleCoating.Density = double.Parse(this.tbDensity.Text, CultureInfo.InvariantCulture);
                OIHelper.SEMQuantSettings.SampleCoating.CoatingElement = int.Parse(this.tbCoatingElement.Text, CultureInfo.InvariantCulture);
            }
            else
            {
                OIHelper.SEMQuantSettings.SampleCoating.IsCoated = false;
            }

            if (this.cbThresholding.Checked)
            {
                OIHelper.SEMQuantSettings.Thresholding = true;
                OIHelper.SEMQuantSettings.SigmaLevel = double.Parse(this.tbSigmaLevel.Text, CultureInfo.InvariantCulture);
            }
            else
            {
                OIHelper.SEMQuantSettings.Thresholding = false;
            }

            OIHelper.SEMQuantSettings.Normalised = this.cbNormalised.Checked;

            this.dgQuantResult.Rows.Clear();
            try
            {
                ISEMQuantStatus quantStatus = OIHelper.EdSpectrumProcessing.SEMQuantifySpectrum(this.spectrumViewer.Spectrum, OIHelper.SEMQuantSettings);

                this.tbQuantStatusMessage.Text = quantStatus.Status.ToString() + System.Environment.NewLine +
                                                 quantStatus.StatusMessage;

                double totalWeightPercent = 0;
                double totalAtomicPercent = 0;
                foreach (ISEMQuantResult result in quantStatus.Results)
                {
                    if (result.WeightPercent != 0)
                    {
                        this.dgQuantResult.Rows.Add(new object[]
                        {
                            ElementProperties.GetElementSymbol(result.AtomicNumber), result.LineType,
                            Math.Round(result.WeightPercent, 2), Math.Round(result.WeightPercentSigma, 6),
                            Math.Round(result.AtomicPercent, 2)
                        });
                    }

                    totalWeightPercent += result.WeightPercent;
                    totalAtomicPercent += result.AtomicPercent;
                }

                this.dgQuantResult.Rows.Add(new object[]
                {
                    @"Total", null, Math.Round(totalWeightPercent, 2), null, Math.Round(totalAtomicPercent, 2)
                });

                this.spectrumViewer.SEMQuantify(OIHelper.SEMQuantSettings);
            }
            catch (QuantificationException ex)
            {
                MessageBox.Show(ex.Message, @"Quantification Error", MessageBoxButtons.OK, MessageBoxIcon.Warning);
            }
            catch (ArgumentNullException)
            {
            }
        }

        /// <summary>
        /// The last element set
        /// </summary>
        private int lastElementSet = -1;

        /// <summary>
        /// ExcludeElementCombo_PropertyChanged
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">PropertyChangedEventArgs</param>
        private void ExcludeElementCombo_PropertyChanged(object sender, PropertyChangedEventArgs e)
        {
            if (e.PropertyName == @"CurrentElement")
            {
                this.UpdateHighlightedElementInTable();
            }
        }

        /// <summary>
        /// Updates the highlighted element in table.
        /// </summary>
        private void UpdateHighlightedElementInTable()
        {
            if (this.lastElementSet != -1)
            {
                this.periodicTableControl.SetElementColor(this.lastElementSet, System.Windows.Media.Colors.Transparent);
            }

            System.Windows.Media.Color currentElementColor = System.Windows.Media.Color.FromArgb(255, 200, 255, 0);

            this.periodicTableControl.SetElementColor(this.excludeElementCombo.CurrentElement, currentElementColor);
            this.periodicTableControl.ShowElementColors = true;
            this.lastElementSet = this.excludeElementCombo.CurrentElement;
        }

        /// <summary>
        /// Add deconvolution element to list
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void AddDeconvolutionButton_Click(object sender, EventArgs e)
        {
            this.tbDeconvolutionElementList.Clear();
            int element = this.deconvolutionElementCombo.CurrentElement;

            try
            {
                OIHelper.SEMQuantSettings.SetDeconvolutionElement(element, true);

                foreach (int i in OIHelper.SEMQuantSettings.DeconvolutionElements)
                {
                    this.tbDeconvolutionElementList.Text += i.ToString(CultureInfo.InvariantCulture) + System.Environment.NewLine;
                }
            }
            catch (FormatException fe)
            {
                this.tbDeconvolutionElementList.Text = fe.Message;
            }
            catch (ArgumentOutOfRangeException ae)
            {
                this.tbDeconvolutionElementList.Text = ae.Message;
            }
        }

        /// <summary>
        /// Remove element from deconvolution list 
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void DeleteDeconvolutionButton_Click(object sender, EventArgs e)
        {
            this.tbDeconvolutionElementList.Clear();
            int element = this.deconvolutionElementCombo.CurrentElement;

            try
            {
                OIHelper.SEMQuantSettings.SetDeconvolutionElement(element, false);

                foreach (int i in OIHelper.SEMQuantSettings.DeconvolutionElements)
                {
                    this.tbDeconvolutionElementList.Text += i.ToString(CultureInfo.InvariantCulture) + System.Environment.NewLine;
                }
            }
            catch (FormatException fe)
            {
                this.tbDeconvolutionElementList.Text = fe.Message;
            }
        }

        /// <summary>
        /// Clear deconvolution elements
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void ClearListButton_Click(object sender, EventArgs e)
        {
            this.tbDeconvolutionElementList.Clear();
            OIHelper.SEMQuantSettings.ClearDeconvolutionElements();

            foreach (int i in OIHelper.SEMQuantSettings.DeconvolutionElements)
            {
                this.tbDeconvolutionElementList.Text += i.ToString(CultureInfo.InvariantCulture) + System.Environment.NewLine;
            }
        }

        /// <summary>
        /// Used when processing spectra from specimens in which all elements yield X-rays which can be readily detected. 
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void AllElementsRadiobutton_Click(object sender, EventArgs e)
        {
            OIHelper.SEMQuantSettings.ProcessingOption = ProcessingOption.AllElements;
            this.cbNormalised.Enabled = true;
            this.tbCombinedElement.Enabled = false;
            this.tbNumberOfIons.Enabled = false;
        }

        /// <summary>
        /// Calculated assuming that the difference between the analyzed total and 100%
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void ElementByDifferenceRadioButton_Click(object sender, EventArgs e)
        {
            OIHelper.SEMQuantSettings.ProcessingOption = ProcessingOption.ElementByDifference;
            this.cbNormalised.Checked = false;
            this.cbNormalised.Enabled = false;
            this.tbCombinedElement.Enabled = true;
            this.tbNumberOfIons.Enabled = false;
        }

        /// <summary>
        /// Concentration of oxygen to be calculated.
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void ElementByStoichiometryRadiobutton_Click(object sender, EventArgs e)
        {
            OIHelper.SEMQuantSettings.ProcessingOption = ProcessingOption.ElementByStoichiometry;
            this.cbNormalised.Enabled = true;
            this.tbCombinedElement.Enabled = false;
            this.tbNumberOfIons.Enabled = true;
        }

        /// <summary>
        /// ThresholdingCheckbox checked
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void ThresholdingCheckbox_CheckedChanged(object sender, EventArgs e)
        {
            this.tbSigmaLevel.Enabled = this.cbThresholding.Checked;
        }

        /// <summary>
        /// IsCoatedCheckbox checked
        /// </summary>
        /// <param name="sender">sender object</param>
        /// <param name="e">EventArgs</param>
        private void IsCoatedCheckbox_CheckedChanged(object sender, EventArgs e)
        {
            this.tbCoatingElement.Enabled = this.cbIsCoated.Checked;
            this.tbDensity.Enabled = this.cbIsCoated.Checked;
            this.tbThickness.Enabled = this.cbIsCoated.Checked;
        }

        #endregion

        #endregion

        #region Periodic Table

        /// <summary>
        /// Handles the CollectionChanged event of the PeriodicTableExcludedElements control.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="NotifyCollectionChangedEventArgs"/> instance containing the event data.</param>
        private void PeriodicTableExcludedElements_CollectionChanged(object sender, NotifyCollectionChangedEventArgs e)
        {
            this.UpdateElementsList(this.periodicTableControl.ExcludedElements, this.tbExcludedElementList);
        }

        /// <summary>
        /// Handles the CollectionChanged event of the PeriodicTableIncludedElements control.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="NotifyCollectionChangedEventArgs"/> instance containing the event data.</param>
        private void PeriodicTableIncludedElements_CollectionChanged(object sender, NotifyCollectionChangedEventArgs e)
        {
            this.UpdateElementsList(this.periodicTableControl.IncludedElements, this.tbIncludedElementList);

            var spectrum = this.spectrumViewer.Spectrum;
            if (spectrum != null)
            {
                switch (e.Action)
                {
                    case NotifyCollectionChangedAction.Add:
                        foreach (int i in e.NewItems.Cast<int>())
                        {
                            spectrum.SetIdentifiedElement(i, true);
                        }

                        break;
                    case NotifyCollectionChangedAction.Remove:
                        foreach (int i in e.OldItems.Cast<int>())
                        {
                            spectrum.SetIdentifiedElement(i, false);
                        }

                        break;
                    default:
                        break;
                }

                this.UpdateSpectrumPeakLabels();
            }
        }

        /// <summary>
        /// Handles the CollectionChanged event of the PeriodicTableUnsetElements control.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="NotifyCollectionChangedEventArgs"/> instance containing the event data.</param>
        private void PeriodicTableUnsetElements_CollectionChanged(object sender, NotifyCollectionChangedEventArgs e)
        {
            this.UpdateElementsList(this.periodicTableControl.UnsetElements, this.tbUnsetElementList);
        }

        /// <summary>
        /// Handles the CheckedChanged event of the EnableMultiselectToolStripMenuItem control.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void EnableMultiselectToolStripMenuItem_CheckedChanged(object sender, EventArgs e)
        {
            this.periodicTableControl.SelectionMode = this.enableMultiselectToolStripMenuItem.Checked ?
                System.Windows.Controls.SelectionMode.Multiple : System.Windows.Controls.SelectionMode.Single;
        }

        /// <summary>
        /// Handles the SelectedIndexChanged event of the PeriodicTableBackgroundToolStripComboBox control.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void PeriodicTableBackgroundToolStripComboBox_SelectedIndexChanged(object sender, EventArgs e)
        {
            if (this.periodicTableBackgroundToolStripComboBox.SelectedItem != null)
            {
                System.Drawing.Color selectedColor = System.Drawing.Color.FromKnownColor((System.Drawing.KnownColor)this.periodicTableBackgroundToolStripComboBox.SelectedItem);

                this.periodicTableElementHost.BackColor = selectedColor;
                this.periodicTableBackgroundToolStripComboBox.BackColor = selectedColor;
                this.periodicTableBackgroundToolStripComboBox.ForeColor = selectedColor.ToArgb() > (0xFFFFFFFF / 2) ? System.Drawing.Color.Black : System.Drawing.Color.LightGray;
            }
        }

        /// <summary>
        /// Initializes the enabled elements menu items.
        /// </summary>
        private void InitializeEnabledElementsMenuItems()
        {
            ToolStripMenuItem item;

            for (int element = 1; element <= 103; element++)
            {
                IPeriodicTableElement info = this.periodicTableControl.LookupElementInfo(element);
                if (info != null)
                {
                    item = new ToolStripMenuItem(info.ElementName);
                    item.CheckOnClick = true;
                    item.Checked = true;
                    item.Tag = element;
                    item.CheckedChanged += this.ElementEnabled_CheckedChanged;
                    this.enabledElementsMenuItem.DropDownItems.Add(item);
                }
            }
        }

        /// <summary>
        /// Handles the CheckedChanged event of the ElementEnabled control.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void ElementEnabled_CheckedChanged(object sender, EventArgs e)
        {
            ToolStripMenuItem menuItem = sender as ToolStripMenuItem;

            if (menuItem != null)
            {
                int elementNo = (int)menuItem.Tag;

                this.periodicTableControl.EnableElements(menuItem.Checked, elementNo);
            }
        }

        #endregion

        /// <summary>
        /// Handles the SelectedIndexChanged event of the CbCompareColor control.
        /// </summary>
        /// <param name="sender">The source of the event.</param>
        /// <param name="e">The <see cref="System.EventArgs"/> instance containing the event data.</param>
        private void CbCompareColor_SelectedIndexChanged(object sender, EventArgs e)
        {
            this.addCompareSpectraButton.BackColor = Color.FromKnownColor((KnownColor)this.cbCompareColor.SelectedItem);
        }

        /// <summary>
        /// Called when [image tool ComboBox selected index changed].
        /// </summary>
        /// <param name="sender">The sender.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void OnImageToolComboBoxSelectedIndexChanged(object sender, EventArgs e)
        {
            if (this.imageViewer != null)
            {
                this.imageViewer.InteractionTool = (ImageInteractionTool)this.imageToolComboBox.SelectedItem;
            }
        }

        /// <summary>
        /// Called when [spectrum tool ComboBox selected index changed].
        /// </summary>
        /// <param name="sender">The sender.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void OnSpectrumToolComboBoxSelectedIndexChanged(object sender, EventArgs e)
        {
            if (this.spectrumViewer != null)
            {
                this.spectrumViewer.InteractionTool = (InteractionTool)this.spectrumInteractionToolComboBox.SelectedItem;
            }
        }

        /// <summary>
        /// Adds a spectrum for comparison.
        /// </summary>
        /// <param name="sender">The sender.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void OnAddCompareSpectraButtonClick(object sender, EventArgs e)
        {
            var spectrum = this.cbCompareSpectraComboBox.SelectedItem as IEdSpectrum;

            if (spectrum != null)
            {
                // Add Current Spectrum to Compare source
                WindowsMedia.Color spectrumColor = ColorConverter.Convert(this.addCompareSpectraButton.BackColor);
                this.spectrumViewer.AddComparisonSpectrum(spectrum, spectrumColor);
                this.cbCompareColor.SelectedItem = GetRandomColor();
            }
        }

        /// <summary>
        /// Loads the comparison spectra.
        /// </summary>
        private void LoadComparisonSpectra()
        {
            byte[] data;

            this.comparisonSpectra = new List<IEdSpectrum>();

            using (FileStream file = new FileStream(@"ComparisonSpectra\Nickel.spec", FileMode.Open))
            {
                data = new byte[file.Length];
                file.Read(data, 0, (int)file.Length);
                this.comparisonSpectra.Add(DataFactory.LoadEdSpectrum(data));
            }

            using (FileStream file = new FileStream(@"ComparisonSpectra\Preview spectrum.spec", FileMode.Open))
            {
                data = new byte[file.Length];
                file.Read(data, 0, (int)file.Length);
                this.comparisonSpectra.Add(DataFactory.LoadEdSpectrum(data));
            }

            using (FileStream file = new FileStream(@"ComparisonSpectra\Tungsten particle.spec", FileMode.Open))
            {
                data = new byte[file.Length];
                file.Read(data, 0, (int)file.Length);
                this.comparisonSpectra.Add(DataFactory.LoadEdSpectrum(data));
            }

            this.cbCompareSpectraComboBox.DataSource = this.comparisonSpectra;
            this.cbCompareSpectraComboBox.DisplayMember = @"Label";
            this.cbCompareSpectraComboBox.SelectedIndex = 0;
        }

        /// <summary>
        /// Called when [clear excluded list button clicked].
        /// </summary>
        /// <param name="sender">The sender.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void OnClearExcludedListButtonClicked(object sender, EventArgs e)
        {
            foreach (int element in this.periodicTableControl.ExcludedElements)
            {
                this.periodicTableControl.Clear(element);
            }

            this.UpdateElementsList(this.periodicTableControl.ExcludedElements, this.tbExcludedElementList);
        }

        /// <summary>
        /// Called when [export tiff button clicked].
        /// </summary>
        /// <param name="sender">The sender.</param>
        /// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
        private void OnExportTiffButtonClicked(object sender, EventArgs e)
        {
            // Export a tiff synchronously on the calling thread.
            var syncTiff = this.spectrumViewer.CreateImage(ExportImageType.Tiff);
            File.WriteAllBytes(Path.Combine(Path.GetTempPath(), @"zSpectrumSync.tiff"), syncTiff);

            // Export a tiff asynchronously on a background thread.
            // The thread must be created with an apartment state set to STA.
            // Calls to CreateImage() must be made on the same thread that created the viewer.
            var spectrum = this.spectrumViewer.Spectrum;
            var thread = new System.Threading.Thread(() =>
            {
                // For optimum performance, create a single spectrum viewer and change the spectrum
                // and viewer settings where required for all spectra that you need images for.
                var backgroundViewer = new SpectrumViewer();

                // A height and width must be set to provide the image dimensions in pixels.
                backgroundViewer.Width = 500;
                backgroundViewer.Height = 500;

                backgroundViewer.IsYAxisAutoScaleEnabled = true;
                backgroundViewer.YAxisType = ScaleType.Logarithmic;
                backgroundViewer.MaximumEnergy = 8;
                backgroundViewer.Spectrum = spectrum;

                var asyncTiff = backgroundViewer.CreateImage(ExportImageType.Tiff);
                File.WriteAllBytes(Path.Combine(Path.GetTempPath(), @"zSpectrumAsync.tiff"), asyncTiff);

                backgroundViewer.Dispatcher.InvokeShutdown();
            });

            thread.IsBackground = true;
            thread.SetApartmentState(ApartmentState.STA);
            thread.Start();
        }
    }
}