/*
 * Copyright (c) 2014 Paul Scherrer Institute. All rights reserved.
 */

import ch.psi.pshell.core.Context;
import ch.psi.pshell.device.Device;
import ch.psi.pshell.device.DeviceAdapter;
import ch.psi.pshell.device.DeviceListener;
import ch.psi.pshell.device.Writable;
import ch.psi.pshell.epics.AreaDetector;
import ch.psi.pshell.plot.LinePlotSeries;
import ch.psi.pshell.plot.RangeSelectionPlot.RangeSelection;
import ch.psi.pshell.ui.Panel;
import ch.psi.utils.Convert;
import ch.psi.utils.IO;
import ch.psi.utils.Serializer;
import ch.psi.utils.State;
import ch.psi.utils.swing.SwingUtils;
import ch.psi.pshell.swing.ValueSelection;
import ch.psi.pshell.swing.ValueSelection.ValueSelectionListener;
import ch.psi.pshell.ui.ScriptProcessor;
import java.awt.Component;
import java.io.File;
import java.lang.reflect.Method;
import java.nio.file.Files;
import java.time.LocalTime;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JToggleButton;
import javax.swing.SwingUtilities;
import javax.swing.event.TableModelEvent;
import javax.swing.event.TableModelListener;
import javax.swing.filechooser.FileNameExtensionFilter;
import javax.swing.table.DefaultTableModel;

/**
 *
 */
public class XPSSpectrum extends ScriptProcessor {

    boolean detailedScan;
    boolean running;
    AreaDetector scienta;
    SwingUtils.TableChangeListener tableChangeListener;
    
    boolean showMiddle = false;
    int indexTime = showMiddle? 3 :2;
    int indexSize = showMiddle? 4 :3;
    int indexIter = showMiddle? 5 :4;    
    int indexEph = showMiddle? 6 :5;    

    public XPSSpectrum() {
        initComponents();        
        rangeSelectionPanel.setOverlapAllowed(true);
        rangeSelectionPanel.setDuplicateAllowed(true);
        rangeSelectionPanel.setShowMiddle(showMiddle);
        buttonSkip.setVisible(false);
        rangeSelectionPanel.setAditionalColumns(new String[]{"Time", "Size", "Iter", "Eph", "Name"}, new Class[]{Double.class, Double.class, Integer.class, Double.class, String.class});
        final DefaultTableModel model = (DefaultTableModel) rangeSelectionPanel.getTable().getModel();
        model.addTableModelListener(new TableModelListener() {
            @Override
            public void tableChanged(TableModelEvent e) {
                if (e.getType() == TableModelEvent.INSERT) {
                    final int row = e.getFirstRow();
                    final int col = e.getColumn();
                    SwingUtilities.invokeLater(new Runnable() {

                        @Override
                        public void run() {
                            if (col<model.getColumnCount()){
                                if (row > 0) {
                                    for (int col = indexTime; col <=indexEph; col++) {
                                        model.setValueAt(model.getValueAt(row - 1, col), row, col);
                                    }
                                } else if (row == 0) {
                                    model.setValueAt(valueTime.getValue(), row, indexTime);
                                    model.setValueAt(valueSize.getValue(), row, indexSize);
                                    model.setValueAt((int) valueIterations.getValue(), row, indexIter);
                                    model.setValueAt(Double.NaN, row, indexEph);
                                }
                            }
                        }
                    });
                    }
                }
        });        
        

        //Component persistence
        ArrayList<Component> persistedComponents = new ArrayList<>();
        persistedComponents.addAll(Arrays.asList(SwingUtils.getComponentsByType(this, JToggleButton.class)));
        persistedComponents.addAll(Arrays.asList(SwingUtils.getComponentsByType(this, ValueSelection.class)));
        persistedComponents.addAll(Arrays.asList(SwingUtils.getComponentsByType(this, JComboBox.class)));
        setPersistedComponents(persistedComponents.toArray(new Component[0]));
        
        ValueSelectionListener listener = new ValueSelectionListener() {
            @Override
            public void onValueChanged(ValueSelection origin, double value, boolean editing) {
                try{
                    if (editing){
                        if (scienta!=null){
                            if (origin == valueLow){
                                ((Writable)scienta.getChild(scienta.getName() + " low energy")).write(value);
                            } else if (origin == valueHigh){
                                ((Writable)scienta.getChild(scienta.getName() + " high energy")).write(value);
                            } else if (origin == valueTime){
                                ((Writable)scienta.getChild(scienta.getName() + " exposure time")).write(value);
                            } else if (origin == valueSize){
                                ((Writable)scienta.getChild(scienta.getName() + " step size")).write(value);
                            }
                        }
                    }
                } catch (Exception ex){
                    getLogger().log(Level.WARNING, null, ex);
                }
            }
        };
        
        valueLow.addListener(listener);
        valueHigh.addListener(listener);
        valueTime.addListener(listener);
        valueSize.addListener(listener);       


        tableChangeListener = new SwingUtils.TableChangeListener(rangeSelectionPanel.getTable()) {
            @Override
            protected void onTableChange(int row, int column, Object value, Object former) {
                if ((checkCIS.isSelected()) && (column == indexEph)){
                    try{
                        if (!isDefined (value)){
                            value = XPSSpectrum.this.getDevice("Eph").take();
                        }
                        if (!isDefined (former)){
                            former = XPSSpectrum.this.getDevice("Eph").take();
                        }
                        if (isDefined (value) && isDefined (former) && (!value.equals(former))){
                            double offset = ((Double)value) - ((Double)former);
                            Double lower = (Double) model.getValueAt(row, 0);
                            Double upper = (Double) model.getValueAt(row, indexTime-1);
                            if ( isDefined (lower) && isDefined (upper)){                                                                                            
                                model.setValueAt(lower + offset, row, 0);
                                model.setValueAt(upper + offset, row, indexTime-1);    
                                RangeSelection range = rangeSelectionPanel.getPlotRange(lower, null, upper);
                                if (range!=null){
                                    rangeSelectionPanel.getPlot().updateRange(range, lower + offset, upper + offset);
                                }
                            }                        
                        }
                    } catch (Exception ex) {
                        showException(ex);
                    } 
                }
            }
        };
      
    }
    
    boolean isDefined(Object value){
        return (value != null) && (value instanceof Double) && !(((Double)value).isNaN());
    }

    @Override
    public void onInitialize(int runCount) {
        scienta = (AreaDetector) getDevice("Scienta");
        
        try {
            if (scienta.getChild(scienta.getName() + " current step")!=null){
                scienta.getChild(scienta.getName() + " current step").addListener(progressListener);
                scienta.getChild(scienta.getName() + " total steps").addListener(progressListener);
            } else  {
                scienta.getChild(scienta.getName() + " current channel").addListener(progressListener);
                scienta.getChild(scienta.getName() + " total points").addListener(progressListener);
            }
            dvpAcqTime.setDevice((Device)getScienta("getAcquisitionTime"));
            comboPass.setSelectedItem((Integer)getScienta("getPassEnergy"));
        } catch (Exception ex) {
            Logger.getLogger(XPSSpectrum.class.getName()).log(Level.SEVERE, null, ex);
        }
        startTimer(500, 100);        
        manualInitPlotData();        
    }
    
    void manualInitPlotData(){
        //Setting data so cam define ranges for detailed without initial
        LinePlotSeries series = new LinePlotSeries("Data");
        rangeSelectionPanel.setSeries(series);                                
        series.setData(new double[]{valueLow.getValue(), valueHigh.getValue()}, new double[]{Double.NaN,Double.NaN});                
    }
            
    @Override
    public void onStateChange(State state, State former) {
        setEnabled(state == State.Ready);
        if (!state.isProcessing()) {
            buttonSkip.setVisible(false);
            if (running) {
                //stopTimer();
                running = false;
                getView().getStatusBar().setProgress(-1);
            }
        }
    }

    @Override
    public void onExecutedFile(String fileName, Object result) {
        String script = IO.getPrefix(fileName);
        if (script != null) {
            switch (script) {
                case "XPSSpectrum":
                    if (result instanceof Exception) {
                        //SwingUtils.showMessage(getComponent(), "Error in " + fileName, exception.getMessage());
                        if (detailedScan) {

                        } else {
                            manualInitPlotData();
                        }
                    } else {
                        if (detailedScan) {

                        } else {
                            Object[] ret = (Object[]) ((Object[]) result)[0];
                            if (ret.length > 0) {
                                double[] xdata = (double[]) Convert.toPrimitiveArray(ret[0], Double.class);
                                double[] ydata = (double[]) Convert.toPrimitiveArray(ret[1], Double.class);

                                //double[] xdata = (double[]) ret[0];
                                //double[] ydata = (double[]) ret[1];

                                //double[] data = new double[]{1.0,1.0,1.0,1.0,1.0};
                                LinePlotSeries series = new LinePlotSeries("Data");
                                rangeSelectionPanel.setSeries(series);
                                series.setData(xdata, ydata);
                            }
                        }
                    }
                    break;
            }
        }
        detailedScan = false;
        updateButtons();
    }

    @Override
    public void setEnabled(boolean value) {
        super.setEnabled(value);
        rangeSelectionPanel.setEnabled(value);
        valueLow.setEnabled(value);
        valueHigh.setEnabled(value);
        valueTime.setEnabled(value);
        valueSize.setEnabled(value);
        valueIterations.setEnabled(value);
        comboPass.setEnabled(value);
        checkEndScan.setEnabled(value);
        checkSaveImage.setEnabled(value);
        updateButtons();
    }

    void updateButtons() {
        buttonStart.setEnabled(isEnabled());
        radioInitial.setEnabled(isEnabled());
        radioDetailed.setEnabled(isEnabled() && rangeSelectionPanel.getPlot().getSelectedRanges().length > 0);
        if (!radioDetailed.isEnabled()){
            radioInitial.setSelected(true);
        }
        btLoad.setEnabled(isEnabled());
        btSave.setEnabled(radioDetailed.isEnabled());
    }

    DeviceListener progressListener = new DeviceAdapter() {

        @Override
        public void onValueChanged(Device device, Object o, Object o1) {
            if (running) {
                try {
                    getView().getStatusBar().setProgress((Double)getScienta("getProgress"));
                } catch (Exception ex) {
                    Logger.getLogger(XPSSpectrum.class.getName()).log(Level.WARNING, null, ex);
                }
            }
        }
    };
    public final String CURRERNT_RANGE_VAR = "cur_range";
    public final String CURRERNT_ITERATION_VAR = "cur_iteration";
    int currentScanIndex;
    RangeSelection[] scanRanges;

    @Override
    protected void onTimer() {
        try {
            if (running) {
                Object index = XPSSpectrum.this.eval(CURRERNT_RANGE_VAR, true);
                if ((index != null) && (index instanceof Integer) && ((Integer) index >= 0)) {
                    int scanIndex = (Integer) index;
                    if (scanIndex != currentScanIndex) {
                        buttonSkip.setEnabled(true);
                    }
                    currentScanIndex = scanIndex;

                    int current_iteration = (Integer) XPSSpectrum.this.eval(CURRERNT_ITERATION_VAR, true);
                    int iterations = (Integer) scanRanges[currentScanIndex].getVars()[2];

                    buttonSkip.setVisible((iterations > 1) && (current_iteration < (iterations - 1)));

                    if (detailedScan) {
                        RangeSelection range = rangeSelectionPanel.getRanges()[scanIndex];
                        for (int row = 0; row < rangeSelectionPanel.getTable().getRowCount(); row++) {
                            if (range.equals((Double) rangeSelectionPanel.getTable().getValueAt(row, 0), (Double) rangeSelectionPanel.getTable().getValueAt(row, 2))) {
                                rangeSelectionPanel.getTable().setRowSelectionInterval(row, row);
                                break;
                            }
                            if (row == (rangeSelectionPanel.getTable().getRowCount() - 1)) {
                                rangeSelectionPanel.getTable().clearSelection();
                            }
                        }
                    }
                } else {
                    rangeSelectionPanel.getTable().clearSelection();
                }
            } else {
                try{
                    int steps = 0;
                    RangeSelection[] r = rangeSelectionPanel.getRanges();
                    if ((radioDetailed.isEnabled()) && (r.length > 0)) {
                        for (int i = 0; i < r.length; i++) {
                            int iterations = (Integer) r[i].getVars()[2];
                            steps += iterations;
                        }
                    } else {
                        steps = Math.max(1, (int) valueIterations.getValue());
                    }
                    int seconds = (int) (Double.valueOf(dvpAcqTime.getLabel().getText()) * steps);
                    int hours = seconds / (60 * 60);
                    textTotalTime.setText(hours >= 24 ? hours + "h" : LocalTime.ofSecondOfDay(seconds).toString());
                } catch (Exception ex) {
                    textTotalTime.setText("");
                }
            }
        } catch (Exception ex) {
            getLogger().log(Level.FINE, null, ex);
        }
    }
    
    @Override
    public String getScript() {
        return "XPSSpectrum";
    }

    @Override
    public Map<String, Object> getArgs() {
        if (radioInitial.isSelected()){
            RangeSelection initialRange = new RangeSelection(valueLow.getValue(), valueHigh.getValue());
            int iterations = (int) valueIterations.getValue();
            initialRange.setVars(new Object[]{valueTime.getValue(), valueSize.getValue(), iterations, Double.NaN});
            scanRanges = new RangeSelection[]{initialRange};
            rangeSelectionPanel.clear(); //TODO: should be done in execute?
        } else {
            scanRanges = rangeSelectionPanel.getRanges();
        }
        detailedScan = !radioInitial.isSelected();
              
        HashMap<String, Object> args = new HashMap<>();
        args.put("DETAILED", !detailedScan);
        args.put("ranges", scanRanges);
        args.put("pass_energy", Integer.valueOf(comboPass.getSelectedItem().toString()));
        args.put("save_scienta_image", checkSaveImage.isSelected());
        args.put("ENDSCAN", checkEndScan.isSelected());         
        return args;
    }        
    
    @Override
    public void execute() throws Exception {
        currentScanIndex = -1;  
        super.execute();
        running = true;
    }            
    
    Object getScienta(String method) throws Exception{
        Method m = scienta.getClass().getMethod(method, new Class[0]);
        return m.invoke(scienta);
    }
    
    void setScienta(String method, Object obj) throws Exception{
        Method m = scienta.getClass().getMethod(method, new Class[]{obj.getClass()});
        m.invoke(scienta, new Object[]{obj});
    }

    
    @SuppressWarnings("unchecked")
    // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
    private void initComponents() {

        buttonGroup1 = new javax.swing.ButtonGroup();
        panelArguments = new javax.swing.JPanel();
        jLabel1 = new javax.swing.JLabel();
        valueIterations = new ch.psi.pshell.swing.ValueSelection();
        jLabel9 = new javax.swing.JLabel();
        valueTime = new ch.psi.pshell.swing.ValueSelection();
        comboPass = new javax.swing.JComboBox();
        valueSize = new ch.psi.pshell.swing.ValueSelection();
        jLabel11 = new javax.swing.JLabel();
        valueLow = new ch.psi.pshell.swing.ValueSelection();
        jLabel2 = new javax.swing.JLabel();
        valueHigh = new ch.psi.pshell.swing.ValueSelection();
        jLabel8 = new javax.swing.JLabel();
        jLabel17 = new javax.swing.JLabel();
        buttonScientaSetup = new javax.swing.JButton();
        checkEndScan = new javax.swing.JCheckBox();
        checkSaveImage = new javax.swing.JCheckBox();
        textTotalTime = new javax.swing.JLabel();
        dvpAcqTime = new ch.psi.pshell.swing.DeviceValuePanel();
        labelAcqTime = new javax.swing.JLabel();
        labelTotalTime = new javax.swing.JLabel();
        jPanel2 = new javax.swing.JPanel();
        btLoad = new javax.swing.JButton();
        btSave = new javax.swing.JButton();
        buttonStart = new javax.swing.JButton();
        rangeSelectionPanel = new ch.psi.pshell.swing.RangeSelectionPanel() {
            protected void onSeriesChanged() {
                updateButtons();
            }
            protected void onSelectionChanged() {
                updateButtons();
            }
        }
        ;
        buttonAbort = new javax.swing.JButton();
        buttonSkip = new javax.swing.JButton();
        checkCIS = new javax.swing.JCheckBox();
        radioInitial = new javax.swing.JRadioButton();
        radioDetailed = new javax.swing.JRadioButton();

        panelArguments.setBorder(javax.swing.BorderFactory.createTitledBorder("Arguments"));

        jLabel1.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
        jLabel1.setText("Low:");

        valueIterations.setDecimals(0);
        valueIterations.setMaxValue(1000.0);
        valueIterations.setMinValue(0.0);
        valueIterations.setShowButtons(false);
        valueIterations.setValue(1.0);

        jLabel9.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
        jLabel9.setText("Size:");

        valueTime.setDecimals(3);
        valueTime.setMaxValue(1000.0);
        valueTime.setMinValue(0.0);
        valueTime.setShowButtons(false);
        valueTime.setValue(1.0);

        comboPass.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "2", "5", "10", "20", "50", "100", "200" }));
        comboPass.setSelectedIndex(4);
        comboPass.setToolTipText("");
        comboPass.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                comboPassActionPerformed(evt);
            }
        });

        valueSize.setDecimals(3);
        valueSize.setMaxValue(1000.0);
        valueSize.setMinValue(0.0);
        valueSize.setShowButtons(false);
        valueSize.setValue(1.0);

        jLabel11.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
        jLabel11.setText("Pass:");

        valueLow.setDecimals(3);
        valueLow.setMaxValue(2000.0);
        valueLow.setMinValue(0.0);
        valueLow.setShowButtons(false);
        valueLow.setValue(0.0);

        jLabel2.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
        jLabel2.setText("High:");

        valueHigh.setDecimals(3);
        valueHigh.setMaxValue(2000.0);
        valueHigh.setMinValue(0.0);
        valueHigh.setShowButtons(false);
        valueHigh.setValue(100.0);

        jLabel8.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
        jLabel8.setText("Time:");

        jLabel17.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
        jLabel17.setText("Iter:");

        buttonScientaSetup.setText("Scienta Setup");
        buttonScientaSetup.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                buttonScientaSetupActionPerformed(evt);
            }
        });

        checkEndScan.setText("Turn off beam at end");

        checkSaveImage.setText("Save Scienta image");

        textTotalTime.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
        textTotalTime.setBorder(javax.swing.BorderFactory.createTitledBorder(""));

        labelAcqTime.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
        labelAcqTime.setText("Acquisition time(s):");

        labelTotalTime.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
        labelTotalTime.setText("Total time:");

        javax.swing.GroupLayout panelArgumentsLayout = new javax.swing.GroupLayout(panelArguments);
        panelArguments.setLayout(panelArgumentsLayout);
        panelArgumentsLayout.setHorizontalGroup(
            panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(panelArgumentsLayout.createSequentialGroup()
                .addContainerGap()
                .addGroup(panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(buttonScientaSetup, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                    .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, panelArgumentsLayout.createSequentialGroup()
                        .addGap(0, 0, Short.MAX_VALUE)
                        .addGroup(panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                            .addComponent(labelAcqTime)
                            .addComponent(labelTotalTime))
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addGroup(panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                            .addComponent(textTotalTime, javax.swing.GroupLayout.Alignment.TRAILING)
                            .addComponent(dvpAcqTime, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.PREFERRED_SIZE, 76, javax.swing.GroupLayout.PREFERRED_SIZE)))
                    .addGroup(panelArgumentsLayout.createSequentialGroup()
                        .addGroup(panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                            .addComponent(checkEndScan)
                            .addComponent(checkSaveImage)
                            .addGroup(panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
                                .addGroup(javax.swing.GroupLayout.Alignment.LEADING, panelArgumentsLayout.createSequentialGroup()
                                    .addComponent(jLabel11)
                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                    .addComponent(comboPass, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
                                .addGroup(javax.swing.GroupLayout.Alignment.LEADING, panelArgumentsLayout.createSequentialGroup()
                                    .addComponent(jLabel17)
                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                    .addComponent(valueIterations, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
                                .addGroup(javax.swing.GroupLayout.Alignment.LEADING, panelArgumentsLayout.createSequentialGroup()
                                    .addComponent(jLabel9)
                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                    .addComponent(valueSize, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
                                .addGroup(javax.swing.GroupLayout.Alignment.LEADING, panelArgumentsLayout.createSequentialGroup()
                                    .addComponent(jLabel8)
                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                    .addComponent(valueTime, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
                                .addGroup(javax.swing.GroupLayout.Alignment.LEADING, panelArgumentsLayout.createSequentialGroup()
                                    .addComponent(jLabel2)
                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                    .addComponent(valueHigh, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
                                .addGroup(javax.swing.GroupLayout.Alignment.LEADING, panelArgumentsLayout.createSequentialGroup()
                                    .addComponent(jLabel1)
                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                    .addComponent(valueLow, javax.swing.GroupLayout.PREFERRED_SIZE, 100, javax.swing.GroupLayout.PREFERRED_SIZE))))
                        .addGap(0, 0, Short.MAX_VALUE)))
                .addContainerGap())
        );

        panelArgumentsLayout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {jLabel1, jLabel11, jLabel17, jLabel2, jLabel8, jLabel9});

        panelArgumentsLayout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {dvpAcqTime, textTotalTime});

        panelArgumentsLayout.setVerticalGroup(
            panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(panelArgumentsLayout.createSequentialGroup()
                .addContainerGap()
                .addGroup(panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
                    .addComponent(valueLow, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(jLabel1))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
                    .addComponent(jLabel2)
                    .addComponent(valueHigh, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(jLabel8)
                    .addComponent(valueTime, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(jLabel9)
                    .addComponent(valueSize, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(jLabel17)
                    .addComponent(valueIterations, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addGap(18, 18, 18)
                .addGroup(panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
                    .addComponent(jLabel11)
                    .addComponent(comboPass, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 32, Short.MAX_VALUE)
                .addGroup(panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
                    .addComponent(labelAcqTime)
                    .addComponent(dvpAcqTime, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(panelArgumentsLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
                    .addComponent(textTotalTime)
                    .addComponent(labelTotalTime))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 32, Short.MAX_VALUE)
                .addComponent(checkEndScan)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(checkSaveImage)
                .addGap(18, 18, 18)
                .addComponent(buttonScientaSetup)
                .addGap(26, 26, 26))
        );

        panelArgumentsLayout.linkSize(javax.swing.SwingConstants.VERTICAL, new java.awt.Component[] {dvpAcqTime, textTotalTime});

        jPanel2.setBorder(javax.swing.BorderFactory.createTitledBorder("Scan Control"));

        btLoad.setText("Load");
        btLoad.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                btLoadActionPerformed(evt);
            }
        });

        btSave.setText("Save");
        btSave.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                btSaveActionPerformed(evt);
            }
        });

        buttonStart.setText("Start");
        buttonStart.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                buttonStartActionPerformed(evt);
            }
        });

        rangeSelectionPanel.setTablePosition(ch.psi.pshell.swing.RangeSelectionPanel.TablePosition.bottom);

        buttonAbort.setText("Abort");
        buttonAbort.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                buttonAbortActionPerformed(evt);
            }
        });

        buttonSkip.setText("Skip");
        buttonSkip.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                buttonSkipActionPerformed(evt);
            }
        });

        checkCIS.setText("Constant Initial State");

        buttonGroup1.add(radioInitial);
        radioInitial.setSelected(true);
        radioInitial.setText("Initial Scan");

        buttonGroup1.add(radioDetailed);
        radioDetailed.setText("Detailed");

        javax.swing.GroupLayout jPanel2Layout = new javax.swing.GroupLayout(jPanel2);
        jPanel2.setLayout(jPanel2Layout);
        jPanel2Layout.setHorizontalGroup(
            jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(jPanel2Layout.createSequentialGroup()
                .addContainerGap()
                .addGroup(jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
                    .addGroup(jPanel2Layout.createSequentialGroup()
                        .addGap(0, 0, Short.MAX_VALUE)
                        .addComponent(btLoad)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                        .addComponent(btSave))
                    .addGroup(javax.swing.GroupLayout.Alignment.LEADING, jPanel2Layout.createSequentialGroup()
                        .addGap(0, 0, 0)
                        .addComponent(radioInitial)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(radioDetailed)
                        .addGap(18, 18, 18)
                        .addComponent(checkCIS)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 70, Short.MAX_VALUE)
                        .addComponent(buttonStart, javax.swing.GroupLayout.PREFERRED_SIZE, 100, javax.swing.GroupLayout.PREFERRED_SIZE)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(buttonSkip)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(buttonAbort))
                    .addComponent(rangeSelectionPanel, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
                .addContainerGap())
        );

        jPanel2Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {btLoad, btSave, buttonAbort, buttonSkip, buttonStart});

        jPanel2Layout.setVerticalGroup(
            jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(jPanel2Layout.createSequentialGroup()
                .addContainerGap()
                .addGroup(jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(buttonStart)
                    .addComponent(buttonAbort)
                    .addComponent(buttonSkip)
                    .addComponent(checkCIS)
                    .addComponent(radioInitial)
                    .addComponent(radioDetailed))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                .addComponent(rangeSelectionPanel, javax.swing.GroupLayout.DEFAULT_SIZE, 294, Short.MAX_VALUE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                .addGroup(jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(btLoad, javax.swing.GroupLayout.Alignment.TRAILING)
                    .addComponent(btSave, javax.swing.GroupLayout.Alignment.TRAILING))
                .addContainerGap())
        );

        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
        this.setLayout(layout);
        layout.setHorizontalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
                .addContainerGap()
                .addComponent(panelArguments, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                .addComponent(jPanel2, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                .addContainerGap())
        );
        layout.setVerticalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(layout.createSequentialGroup()
                .addContainerGap()
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(panelArguments, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                    .addComponent(jPanel2, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
                .addContainerGap())
        );
    }// </editor-fold>//GEN-END:initComponents

    private void buttonAbortActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonAbortActionPerformed
        try {
            abort();
            if (scienta!=null){
                scienta.stop();
            }
        } catch (Exception ex) {
            showException(ex);
        }
    }//GEN-LAST:event_buttonAbortActionPerformed

    private void buttonStartActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonStartActionPerformed
        try {
            execute();
        } catch (Exception ex) {
            showException(ex);
        }

    }//GEN-LAST:event_buttonStartActionPerformed

    private void btSaveActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_btSaveActionPerformed
        try {
            JFileChooser chooser = new JFileChooser(getContext().getSetup().getContextPath());
            FileNameExtensionFilter filter = new FileNameExtensionFilter("XPS Spectrum scan definition file", "xps");
            chooser.setFileFilter(filter);
            int rVal = chooser.showSaveDialog(this);
            if (rVal == JFileChooser.APPROVE_OPTION) {
                File f = chooser.getSelectedFile();
                if (IO.getExtension(f).isEmpty()) {
                    f = new File(f.getPath() + ".xps");
                }
                Object[] obj = new Object[]{SwingUtils.getTableData(rangeSelectionPanel.getTable()),
                    rangeSelectionPanel.getPlot().getSeries(0).getX(),
                    rangeSelectionPanel.getPlot().getSeries(0).getY()};
                Files.write(f.toPath(), Serializer.encode(obj, Serializer.EncoderType.bin));

            }
        } catch (Exception ex) {
            showException(ex);
        }

    }//GEN-LAST:event_btSaveActionPerformed

    private void btLoadActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_btLoadActionPerformed
         try {
            JFileChooser chooser = new JFileChooser(getContext().getSetup().getContextPath());
            FileNameExtensionFilter filter = new FileNameExtensionFilter("XPS Spectrum scan definition file", "xps");
            chooser.setFileFilter(filter);
            int rVal = chooser.showOpenDialog(this);
            if (rVal == JFileChooser.APPROVE_OPTION) {
                rangeSelectionPanel.removeAllRanges();
                Object[] obj = (Object[]) Serializer.decode(Files.readAllBytes(chooser.getSelectedFile().toPath()), Serializer.EncoderType.bin);
                Object[][] table = (Object[][]) obj[0];
                if (!rangeSelectionPanel.getPlot().hasData()) {
                    double[] x = (double[]) obj[1];
                    double[] y = (double[]) obj[2];
                    LinePlotSeries series = new LinePlotSeries("Data");
                    rangeSelectionPanel.setSeries(series);
                    series.setData(x, y);
                }
                int indexUpper;
                int varCols;
                if (table.length>0){
                    boolean hasName = (table[0].length > 6) && (table[0][table[0].length-1] instanceof String);
                    int size_with_center = hasName?8:7;
                    indexUpper = (table[0].length >=size_with_center) ? 2 : 1;
                    varCols = table[0].length - indexUpper-1;
                } else {
                    indexUpper=1;
                    varCols = 0;
                }                
                for (Object[] row : table) {
                    rangeSelectionPanel.getPlot().addRange((Double) row[0], (Double) row[indexUpper]);
                }
                 
                SwingUtilities.invokeLater(new Runnable() {
                    @Override
                    public void run() {
                        for (int row = 0; row < table.length; row++) {                           
                            for (int col = 0; col < varCols; col++) {
                                rangeSelectionPanel.getTable().setValueAt(table[row][col + indexUpper + 1], row, col + indexTime);
                            }
                        }
                    }
                });
            }
        } catch (Exception ex) {
            showException(ex);
        }
    }//GEN-LAST:event_btLoadActionPerformed

    private void buttonSkipActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonSkipActionPerformed
        try {
            this.eval("skip_iteration = True", true);
            buttonSkip.setEnabled(false);
        } catch (Exception ex) {
            showException(ex);
        }
    }//GEN-LAST:event_buttonSkipActionPerformed

    private void buttonScientaSetupActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonScientaSetupActionPerformed
        try {
            showDevicePanel("Scienta");
        } catch (Exception ex) {
            SwingUtils.showException(this, ex);
        }
    }//GEN-LAST:event_buttonScientaSetupActionPerformed

    private void comboPassActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_comboPassActionPerformed
        try {
            if (scienta!=null){
                Integer energy = Integer.valueOf(comboPass.getSelectedItem().toString());
                if (!energy.equals(getScienta("getPassEnergy"))){
                    setScienta("setPassEnergy", energy);            
                }
            }
        } catch (Exception ex) {
            getLogger().log(Level.WARNING, null, ex);
        }        
    }//GEN-LAST:event_comboPassActionPerformed

    // Variables declaration - do not modify//GEN-BEGIN:variables
    private javax.swing.JButton btLoad;
    private javax.swing.JButton btSave;
    private javax.swing.JButton buttonAbort;
    private javax.swing.ButtonGroup buttonGroup1;
    private javax.swing.JButton buttonScientaSetup;
    private javax.swing.JButton buttonSkip;
    private javax.swing.JButton buttonStart;
    private javax.swing.JCheckBox checkCIS;
    private javax.swing.JCheckBox checkEndScan;
    private javax.swing.JCheckBox checkSaveImage;
    private javax.swing.JComboBox comboPass;
    private ch.psi.pshell.swing.DeviceValuePanel dvpAcqTime;
    private javax.swing.JLabel jLabel1;
    private javax.swing.JLabel jLabel11;
    private javax.swing.JLabel jLabel17;
    private javax.swing.JLabel jLabel2;
    private javax.swing.JLabel jLabel8;
    private javax.swing.JLabel jLabel9;
    private javax.swing.JPanel jPanel2;
    private javax.swing.JLabel labelAcqTime;
    private javax.swing.JLabel labelTotalTime;
    private javax.swing.JPanel panelArguments;
    private javax.swing.JRadioButton radioDetailed;
    private javax.swing.JRadioButton radioInitial;
    private ch.psi.pshell.swing.RangeSelectionPanel rangeSelectionPanel;
    private javax.swing.JLabel textTotalTime;
    private ch.psi.pshell.swing.ValueSelection valueHigh;
    private ch.psi.pshell.swing.ValueSelection valueIterations;
    private ch.psi.pshell.swing.ValueSelection valueLow;
    private ch.psi.pshell.swing.ValueSelection valueSize;
    private ch.psi.pshell.swing.ValueSelection valueTime;
    // End of variables declaration//GEN-END:variables
}