import ch.psi.pshell.imaging.Overlay;
import ch.psi.pshell.imaging.Overlays.Rect;
import ch.psi.pshell.imaging.Renderer;
import ch.psi.pshell.imaging.RendererListener;
import ch.psi.pshell.ui.Panel;
import ch.psi.utils.State;
import java.awt.Rectangle;
import java.util.HashMap;

/**
 *
 */
public class Imaging extends Panel {
    static double NaNd = Double.NaN; //Bug on editor?
    
    public Imaging() {
        initComponents();
        renderer.addListener(rendererListener);
    }
            
    //Overridable callbacks
    @Override
    public void onInitialize(int runCount) {
        try {
            setGlobalVar("IMAGING_RENDERER", renderer);
            setRoi(getRoi());            
        } catch (Exception ex) {
            showException(ex);
        }         
    }

    @Override
    public void onStateChange(State state, State former) {
        buttonAbort.setEnabled(state.isProcessing());
        updateButtons();
    }

    @Override
    public void onExecutedFile(String fileName, Object result) {
    }

    
    //Callback to perform update - in event thread
    @Override
    protected void doUpdate() {
    }
    
    void updateButtons(){
        boolean enabled = getState()==State.Ready;
        boolean hasRoi = false;
        try{
            hasRoi = getRoi()!=null;
        } catch (Exception ex){            
        }        
        buttonStartAutoFocus.setEnabled(hasRoi && enabled);
        buttonStartAutoIntensity.setEnabled(enabled);        
        buttonRoiClear.setEnabled(hasRoi && enabled);
        buttonRoiSet.setEnabled(!hasRoi && enabled);
        spinnerAverage.setEnabled(enabled);
        spinnerRuns.setEnabled(enabled);
        spinnerExposition.setEnabled(enabled);
        spinnerRangeObj.setEnabled((radioObjective.isSelected() || radioAll.isSelected()) && enabled);
        spinnerStepObj.setEnabled(spinnerRangeObj.isEnabled());
        spinnerRangeStig.setEnabled((!radioObjective.isSelected()) && enabled);
        spinnerStepStig.setEnabled(spinnerRangeStig.isEnabled());        
        radioObjective.setEnabled(enabled);
        radioStigA.setEnabled(enabled);
        radioStigB.setEnabled(enabled);
        radioAll.setEnabled(enabled);
    }
    
    @Override
    protected void onShow() {
        super.onShow();
        renderer.setDeviceName("image");
        
    }

    @Override
    protected void onHide() {
       super.onHide();
       renderer.setDeviceName(null);
    }    
    
    Rectangle getRoi(){
        return (Rectangle) getGlobalVar("IMAGING_ROI");
    }
    
    void setRoi(Rectangle roi){
        setGlobalVar("IMAGING_ROI", roi);
        try{
            renderer.clearOverlays();                
            if (roi!=null){
                Rect ov = new Rect(renderer.getPenProfile(), roi.getLocation(), roi.getSize());
                ov.setMovable(true);
                renderer.addOverlay(ov);                   
            }
        } finally {
            updateButtons();
        }
    }
    
    
    final RendererListener rendererListener = new RendererListener(){
        @Override
        public void onMoveFinished(Renderer renderer, Overlay overlay) {
            setGlobalVar("IMAGING_ROI", overlay.getBounds());            
        }

        @Override
        public void onDeleted(Renderer renderer, Overlay overlay) {
            if (getRoi()!=null){
                setRoi(null);
            }
        }
    };
    

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

        buttonGroup1 = new javax.swing.ButtonGroup();
        renderer = new ch.psi.pshell.imaging.Renderer();
        jPanel4 = new javax.swing.JPanel();
        jPanel2 = new javax.swing.JPanel();
        buttonStartAutoIntensity = new javax.swing.JButton();
        buttonAbort = new javax.swing.JButton();
        jPanel1 = new javax.swing.JPanel();
        buttonRoiSet = new javax.swing.JButton();
        buttonRoiClear = new javax.swing.JButton();
        jLabel1 = new javax.swing.JLabel();
        spinnerWidth = new javax.swing.JSpinner();
        jLabel2 = new javax.swing.JLabel();
        spinnerHeight = new javax.swing.JSpinner();
        jPanel3 = new javax.swing.JPanel();
        buttonStartAutoFocus = new javax.swing.JButton();
        jLabel3 = new javax.swing.JLabel();
        spinnerAverage = new javax.swing.JSpinner();
        jLabel4 = new javax.swing.JLabel();
        spinnerRuns = new javax.swing.JSpinner();
        jPanel5 = new javax.swing.JPanel();
        radioObjective = new javax.swing.JRadioButton();
        radioStigA = new javax.swing.JRadioButton();
        radioStigB = new javax.swing.JRadioButton();
        radioAll = new javax.swing.JRadioButton();
        jPanel6 = new javax.swing.JPanel();
        spinnerRangeObj = new javax.swing.JSpinner();
        jLabel5 = new javax.swing.JLabel();
        jLabel6 = new javax.swing.JLabel();
        spinnerStepObj = new javax.swing.JSpinner();
        jLabel7 = new javax.swing.JLabel();
        spinnerRangeStig = new javax.swing.JSpinner();
        jLabel8 = new javax.swing.JLabel();
        spinnerStepStig = new javax.swing.JSpinner();
        jLabel9 = new javax.swing.JLabel();
        spinnerExposition = new javax.swing.JSpinner();

        renderer.setMode(ch.psi.pshell.imaging.RendererMode.Fit);

        jPanel2.setBorder(javax.swing.BorderFactory.createTitledBorder("Auto-Intensity"));

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

        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(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                .addComponent(buttonStartAutoIntensity)
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
        );
        jPanel2Layout.setVerticalGroup(
            jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(jPanel2Layout.createSequentialGroup()
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                .addComponent(buttonStartAutoIntensity)
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
        );

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

        jPanel1.setBorder(javax.swing.BorderFactory.createTitledBorder("ROI"));

        buttonRoiSet.setText("Set");
        buttonRoiSet.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                buttonRoiSetActionPerformed(evt);
            }
        });

        buttonRoiClear.setText("Clear");
        buttonRoiClear.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                buttonRoiClearActionPerformed(evt);
            }
        });

        jLabel1.setText("Width:");

        spinnerWidth.setModel(new javax.swing.SpinnerListModel(new String[] {"16", "32", "64", "128", "256", "512"}));
        spinnerWidth.setValue("256");
        spinnerWidth.addChangeListener(new javax.swing.event.ChangeListener() {
            public void stateChanged(javax.swing.event.ChangeEvent evt) {
                spinnerWidthStateChanged(evt);
            }
        });

        jLabel2.setText("Height");

        spinnerHeight.setModel(new javax.swing.SpinnerListModel(new String[] {"16", "32", "64", "128", "256", "512"}));
        spinnerHeight.setValue("256");
        spinnerHeight.addChangeListener(new javax.swing.event.ChangeListener() {
            public void stateChanged(javax.swing.event.ChangeEvent evt) {
                spinnerHeightStateChanged(evt);
            }
        });

        javax.swing.GroupLayout jPanel1Layout = new javax.swing.GroupLayout(jPanel1);
        jPanel1.setLayout(jPanel1Layout);
        jPanel1Layout.setHorizontalGroup(
            jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(jPanel1Layout.createSequentialGroup()
                .addContainerGap()
                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addGroup(jPanel1Layout.createSequentialGroup()
                        .addComponent(buttonRoiClear)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(buttonRoiSet, javax.swing.GroupLayout.PREFERRED_SIZE, 60, javax.swing.GroupLayout.PREFERRED_SIZE)
                        .addGap(18, 18, Short.MAX_VALUE)
                        .addComponent(jLabel1)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(spinnerWidth, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                    .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, jPanel1Layout.createSequentialGroup()
                        .addGap(0, 0, Short.MAX_VALUE)
                        .addComponent(jLabel2)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(spinnerHeight, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))))
        );

        jPanel1Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {jLabel1, jLabel2});

        jPanel1Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {spinnerHeight, spinnerWidth});

        jPanel1Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {buttonRoiClear, buttonRoiSet});

        jPanel1Layout.setVerticalGroup(
            jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(jPanel1Layout.createSequentialGroup()
                .addContainerGap()
                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(buttonRoiClear)
                    .addComponent(buttonRoiSet)
                    .addComponent(jLabel1)
                    .addComponent(spinnerWidth, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(jLabel2)
                    .addComponent(spinnerHeight, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addContainerGap())
        );

        jPanel3.setBorder(javax.swing.BorderFactory.createTitledBorder("Auto-Focus"));

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

        jLabel3.setText("Average:");

        spinnerAverage.setModel(new javax.swing.SpinnerNumberModel(1, 1, 10, 1));
        spinnerAverage.addChangeListener(new javax.swing.event.ChangeListener() {
            public void stateChanged(javax.swing.event.ChangeEvent evt) {
                spinnerAverageStateChanged(evt);
            }
        });

        jLabel4.setText("Runs:");

        spinnerRuns.setModel(new javax.swing.SpinnerNumberModel(1, 0, 10, 1));
        spinnerRuns.addChangeListener(new javax.swing.event.ChangeListener() {
            public void stateChanged(javax.swing.event.ChangeEvent evt) {
                spinnerRunsStateChanged(evt);
            }
        });

        buttonGroup1.add(radioObjective);
        radioObjective.setSelected(true);
        radioObjective.setText("Objective");
        radioObjective.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                radioObjectiveActionPerformed(evt);
            }
        });

        buttonGroup1.add(radioStigA);
        radioStigA.setText("Stigmator A");
        radioStigA.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                radioStigAActionPerformed(evt);
            }
        });

        buttonGroup1.add(radioStigB);
        radioStigB.setText("Stigmator B");
        radioStigB.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                radioStigBActionPerformed(evt);
            }
        });

        buttonGroup1.add(radioAll);
        radioAll.setText("All");
        radioAll.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                radioAllActionPerformed(evt);
            }
        });

        javax.swing.GroupLayout jPanel5Layout = new javax.swing.GroupLayout(jPanel5);
        jPanel5.setLayout(jPanel5Layout);
        jPanel5Layout.setHorizontalGroup(
            jPanel5Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(jPanel5Layout.createSequentialGroup()
                .addContainerGap()
                .addGroup(jPanel5Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(radioObjective)
                    .addComponent(radioStigA)
                    .addComponent(radioStigB)
                    .addComponent(radioAll))
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
        );
        jPanel5Layout.setVerticalGroup(
            jPanel5Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(jPanel5Layout.createSequentialGroup()
                .addGap(0, 0, 0)
                .addComponent(radioObjective)
                .addGap(0, 0, 0)
                .addComponent(radioStigA)
                .addGap(0, 0, 0)
                .addComponent(radioStigB)
                .addGap(0, 0, 0)
                .addComponent(radioAll)
                .addGap(0, 0, 0))
        );

        spinnerRangeObj.setModel(new javax.swing.SpinnerNumberModel(4.0d, 1.0d, 10.0d, 1.0d));
        spinnerRangeObj.addChangeListener(new javax.swing.event.ChangeListener() {
            public void stateChanged(javax.swing.event.ChangeEvent evt) {
                spinnerRangeObjStateChanged(evt);
            }
        });

        jLabel5.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
        jLabel5.setText("Range Objective:");

        jLabel6.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
        jLabel6.setText("Step Objective:");

        spinnerStepObj.setModel(new javax.swing.SpinnerNumberModel(0.2d, 0.1d, 1.0d, 0.1d));
        spinnerStepObj.addChangeListener(new javax.swing.event.ChangeListener() {
            public void stateChanged(javax.swing.event.ChangeEvent evt) {
                spinnerStepObjStateChanged(evt);
            }
        });

        jLabel7.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
        jLabel7.setText("Range Stigmator:");

        spinnerRangeStig.setModel(new javax.swing.SpinnerNumberModel(20.0d, 1.0d, 40.0d, 1.0d));
        spinnerRangeStig.addChangeListener(new javax.swing.event.ChangeListener() {
            public void stateChanged(javax.swing.event.ChangeEvent evt) {
                spinnerRangeStigStateChanged(evt);
            }
        });

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

        spinnerStepStig.setModel(new javax.swing.SpinnerNumberModel(2.0d, 1.0d, 10.0d, 1.0d));
        spinnerStepStig.addChangeListener(new javax.swing.event.ChangeListener() {
            public void stateChanged(javax.swing.event.ChangeEvent evt) {
                spinnerStepStigStateChanged(evt);
            }
        });

        javax.swing.GroupLayout jPanel6Layout = new javax.swing.GroupLayout(jPanel6);
        jPanel6.setLayout(jPanel6Layout);
        jPanel6Layout.setHorizontalGroup(
            jPanel6Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(jPanel6Layout.createSequentialGroup()
                .addContainerGap()
                .addGroup(jPanel6Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addGroup(jPanel6Layout.createSequentialGroup()
                        .addComponent(jLabel5)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(spinnerRangeObj, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                    .addGroup(jPanel6Layout.createSequentialGroup()
                        .addComponent(jLabel6)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(spinnerStepObj, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                    .addGroup(jPanel6Layout.createSequentialGroup()
                        .addComponent(jLabel7)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(spinnerRangeStig, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                    .addGroup(jPanel6Layout.createSequentialGroup()
                        .addComponent(jLabel8)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(spinnerStepStig, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
                .addGap(0, 0, 0))
        );

        jPanel6Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {jLabel5, jLabel6, jLabel7, jLabel8});

        jPanel6Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {spinnerRangeObj, spinnerRangeStig, spinnerStepObj, spinnerStepStig});

        jPanel6Layout.setVerticalGroup(
            jPanel6Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(jPanel6Layout.createSequentialGroup()
                .addGap(0, 0, 0)
                .addGroup(jPanel6Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(jLabel5)
                    .addComponent(spinnerRangeObj, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addGap(0, 0, 0)
                .addGroup(jPanel6Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(jLabel6)
                    .addComponent(spinnerStepObj, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(jPanel6Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(jLabel7)
                    .addComponent(spinnerRangeStig, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addGap(0, 0, 0)
                .addGroup(jPanel6Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(jLabel8)
                    .addComponent(spinnerStepStig, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addContainerGap())
        );

        jLabel9.setText("Exposure:");

        spinnerExposition.setModel(new javax.swing.SpinnerNumberModel(NaNd, 0.01d, NaNd, 1.0d));
        spinnerExposition.addChangeListener(new javax.swing.event.ChangeListener() {
            public void stateChanged(javax.swing.event.ChangeEvent evt) {
                spinnerExpositionStateChanged(evt);
            }
        });

        javax.swing.GroupLayout jPanel3Layout = new javax.swing.GroupLayout(jPanel3);
        jPanel3.setLayout(jPanel3Layout);
        jPanel3Layout.setHorizontalGroup(
            jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(jPanel3Layout.createSequentialGroup()
                .addComponent(jPanel5, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addGap(18, 18, Short.MAX_VALUE)
                .addGroup(jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(jLabel4, javax.swing.GroupLayout.Alignment.TRAILING)
                    .addComponent(jLabel3, javax.swing.GroupLayout.Alignment.TRAILING)
                    .addComponent(jLabel9, javax.swing.GroupLayout.Alignment.TRAILING))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(spinnerAverage, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(spinnerRuns, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(spinnerExposition, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
            .addGroup(jPanel3Layout.createSequentialGroup()
                .addGap(97, 97, 97)
                .addComponent(buttonStartAutoFocus)
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, jPanel3Layout.createSequentialGroup()
                .addGap(0, 0, Short.MAX_VALUE)
                .addComponent(jPanel6, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
        );

        jPanel3Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {spinnerAverage, spinnerExposition, spinnerRuns});

        jPanel3Layout.setVerticalGroup(
            jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(jPanel3Layout.createSequentialGroup()
                .addGroup(jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addGroup(jPanel3Layout.createSequentialGroup()
                        .addGap(4, 4, 4)
                        .addGroup(jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                            .addComponent(jLabel3)
                            .addComponent(spinnerAverage, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                        .addGap(4, 4, 4)
                        .addGroup(jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                            .addComponent(jLabel4)
                            .addComponent(spinnerRuns, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                        .addGap(4, 4, 4)
                        .addGroup(jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                            .addComponent(jLabel9)
                            .addComponent(spinnerExposition, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
                    .addGroup(jPanel3Layout.createSequentialGroup()
                        .addContainerGap()
                        .addComponent(jPanel5, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                .addComponent(jPanel6, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                .addComponent(buttonStartAutoFocus)
                .addContainerGap())
        );

        javax.swing.GroupLayout jPanel4Layout = new javax.swing.GroupLayout(jPanel4);
        jPanel4.setLayout(jPanel4Layout);
        jPanel4Layout.setHorizontalGroup(
            jPanel4Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(jPanel4Layout.createSequentialGroup()
                .addContainerGap()
                .addGroup(jPanel4Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
                    .addComponent(jPanel3, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                    .addComponent(jPanel2, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                    .addComponent(jPanel1, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, jPanel4Layout.createSequentialGroup()
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                .addComponent(buttonAbort)
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
        );
        jPanel4Layout.setVerticalGroup(
            jPanel4Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(jPanel4Layout.createSequentialGroup()
                .addContainerGap()
                .addComponent(jPanel1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jPanel2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jPanel3, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                .addComponent(buttonAbort)
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
        );

        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
        this.setLayout(layout);
        layout.setHorizontalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(layout.createSequentialGroup()
                .addComponent(jPanel4, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(renderer, javax.swing.GroupLayout.DEFAULT_SIZE, 376, Short.MAX_VALUE))
        );
        layout.setVerticalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addComponent(renderer, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
            .addComponent(jPanel4, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
        );
    }// </editor-fold>//GEN-END:initComponents

    private void buttonRoiClearActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonRoiClearActionPerformed
        try {
            setRoi(null);
        } catch (Exception ex) {
           showException(ex);
        }                
    }//GEN-LAST:event_buttonRoiClearActionPerformed

    private void buttonRoiSetActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonRoiSetActionPerformed
        try {
            Rectangle roi = new Rectangle(0,0,Integer.valueOf(spinnerWidth.getValue().toString()),Integer.valueOf(spinnerHeight.getValue().toString()));                        
            setRoi(roi);
        } catch (Exception ex) {
           showException(ex);
        }          
    }//GEN-LAST:event_buttonRoiSetActionPerformed

    private void spinnerWidthStateChanged(javax.swing.event.ChangeEvent evt) {//GEN-FIRST:event_spinnerWidthStateChanged
        try {
            Rectangle roi = getRoi();
            if (roi!=null){
                roi.width = Integer.valueOf(spinnerWidth.getValue().toString());
                setRoi(roi);
            }
            
        } catch (Exception ex) {
           showException(ex);
        }          
    }//GEN-LAST:event_spinnerWidthStateChanged

    private void spinnerHeightStateChanged(javax.swing.event.ChangeEvent evt) {//GEN-FIRST:event_spinnerHeightStateChanged
        try {
            Rectangle roi = getRoi();
            if (roi!=null){
                roi.height = Integer.valueOf(spinnerHeight.getValue().toString());
                setRoi(roi);
            }
            
        } catch (Exception ex) {
           showException(ex);
        }          
    }//GEN-LAST:event_spinnerHeightStateChanged

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

    private void buttonStartAutoFocusActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonStartAutoFocusActionPerformed
        try {
            HashMap args = new HashMap();
            String scan_type = "all";
            if (radioObjective.isSelected()){
                scan_type = "obj";
            } else if (radioStigA.isSelected()){
                scan_type = "stiga";
            } else if (radioStigB.isSelected()){
                scan_type = "stigb";
            }
            int average = (Integer)spinnerAverage.getValue();
            int runs = (Integer)spinnerRuns.getValue();
            Double exposure =  (Double) spinnerExposition.getValue();
            
            //runAsync("templates/AutoFocus", args).handle((ret, t) -> {
            //auto_focus(range_obj=4.0, step_obj=0.2, range_stig=20.0, step_stig=2.0, average=1, runs=2, roi=None):
            String cmd = "auto_focus(scan_type='" + scan_type + "'" +
                            ", range_obj=" + spinnerRangeObj.getValue() +
                            ", step_obj=" + spinnerStepObj.getValue() +
                            ", range_stig=" + spinnerRangeStig.getValue() +
                            ", step_stig=" + spinnerStepStig.getValue() +
                            ", average=" + average + 
                            ", runs=" + runs + 
                            ", renderer=IMAGING_RENDERER"+ 
                            ", roi=IMAGING_ROI"+ 
                            ", exposure=" + (Double.isNaN(exposure) ? "None" : exposure)  + ")";
            this.evalAsync(cmd).handle((ret, t) -> {                        
                if ((t != null) && (!getContext().isAborted())) {
                    showException((Exception) t);
                }
                return t;
            });       
        } catch (Exception ex) {
            showException(ex);
        }
    }//GEN-LAST:event_buttonStartAutoFocusActionPerformed

    private void buttonStartAutoIntensityActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonStartAutoIntensityActionPerformed
        try {            
            //String cmd = "scan_contrast(girder_x, 0.05, 0.005, average=3)";
            String cmd = "auto_intensity(roi=IMAGING_ROI)";
            this.evalAsync(cmd).handle((ret, t) -> {
                if ((t != null) && (!getContext().isAborted())) {
                    showException((Exception) t);
                }
                return t;
            });       
        } catch (Exception ex) {
            showException(ex);
        }
    }//GEN-LAST:event_buttonStartAutoIntensityActionPerformed

    private void spinnerAverageStateChanged(javax.swing.event.ChangeEvent evt) {//GEN-FIRST:event_spinnerAverageStateChanged
        // TODO add your handling code here:
    }//GEN-LAST:event_spinnerAverageStateChanged

    private void spinnerRunsStateChanged(javax.swing.event.ChangeEvent evt) {//GEN-FIRST:event_spinnerRunsStateChanged
        // TODO add your handling code here:
    }//GEN-LAST:event_spinnerRunsStateChanged

    private void radioStigAActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_radioStigAActionPerformed
        updateButtons();
    }//GEN-LAST:event_radioStigAActionPerformed

    private void spinnerRangeObjStateChanged(javax.swing.event.ChangeEvent evt) {//GEN-FIRST:event_spinnerRangeObjStateChanged
        // TODO add your handling code here:
    }//GEN-LAST:event_spinnerRangeObjStateChanged

    private void spinnerStepObjStateChanged(javax.swing.event.ChangeEvent evt) {//GEN-FIRST:event_spinnerStepObjStateChanged
        // TODO add your handling code here:
    }//GEN-LAST:event_spinnerStepObjStateChanged

    private void spinnerRangeStigStateChanged(javax.swing.event.ChangeEvent evt) {//GEN-FIRST:event_spinnerRangeStigStateChanged
        // TODO add your handling code here:
    }//GEN-LAST:event_spinnerRangeStigStateChanged

    private void spinnerStepStigStateChanged(javax.swing.event.ChangeEvent evt) {//GEN-FIRST:event_spinnerStepStigStateChanged
        // TODO add your handling code here:
    }//GEN-LAST:event_spinnerStepStigStateChanged

    private void radioAllActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_radioAllActionPerformed
        updateButtons();
    }//GEN-LAST:event_radioAllActionPerformed

    private void radioObjectiveActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_radioObjectiveActionPerformed
        updateButtons();
    }//GEN-LAST:event_radioObjectiveActionPerformed

    private void radioStigBActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_radioStigBActionPerformed
        updateButtons();
    }//GEN-LAST:event_radioStigBActionPerformed

    private void spinnerExpositionStateChanged(javax.swing.event.ChangeEvent evt) {//GEN-FIRST:event_spinnerExpositionStateChanged
        // TODO add your handling code here:
    }//GEN-LAST:event_spinnerExpositionStateChanged

    // Variables declaration - do not modify//GEN-BEGIN:variables
    private javax.swing.JButton buttonAbort;
    private javax.swing.ButtonGroup buttonGroup1;
    private javax.swing.JButton buttonRoiClear;
    private javax.swing.JButton buttonRoiSet;
    private javax.swing.JButton buttonStartAutoFocus;
    private javax.swing.JButton buttonStartAutoIntensity;
    private javax.swing.JLabel jLabel1;
    private javax.swing.JLabel jLabel2;
    private javax.swing.JLabel jLabel3;
    private javax.swing.JLabel jLabel4;
    private javax.swing.JLabel jLabel5;
    private javax.swing.JLabel jLabel6;
    private javax.swing.JLabel jLabel7;
    private javax.swing.JLabel jLabel8;
    private javax.swing.JLabel jLabel9;
    private javax.swing.JPanel jPanel1;
    private javax.swing.JPanel jPanel2;
    private javax.swing.JPanel jPanel3;
    private javax.swing.JPanel jPanel4;
    private javax.swing.JPanel jPanel5;
    private javax.swing.JPanel jPanel6;
    private javax.swing.JRadioButton radioAll;
    private javax.swing.JRadioButton radioObjective;
    private javax.swing.JRadioButton radioStigA;
    private javax.swing.JRadioButton radioStigB;
    private ch.psi.pshell.imaging.Renderer renderer;
    private javax.swing.JSpinner spinnerAverage;
    private javax.swing.JSpinner spinnerExposition;
    private javax.swing.JSpinner spinnerHeight;
    private javax.swing.JSpinner spinnerRangeObj;
    private javax.swing.JSpinner spinnerRangeStig;
    private javax.swing.JSpinner spinnerRuns;
    private javax.swing.JSpinner spinnerStepObj;
    private javax.swing.JSpinner spinnerStepStig;
    private javax.swing.JSpinner spinnerWidth;
    // End of variables declaration//GEN-END:variables
}