Control panel for running 3B plugin and providing interactive update. More...

Public Member Functions
void	windowOpened (WindowEvent e)
void	windowClosed (WindowEvent e)
void	windowDeactivated (WindowEvent e)
void	windowActivated (WindowEvent e)
void	windowDeiconified (WindowEvent e)
void	windowIconified (WindowEvent e)
void	windowClosing (WindowEvent e)
void	issue_stop ()
synchronized void	append (final ArrayList< Spot > p, int its)
void	send_update_canvas_event ()
void	die (final String s)
void	send_status_text_message (final String s)
void	send_time_text_message (final String s)
Package Functions
	EControlPanel (Rectangle roi_, double ps_, String filename_, ThreeBRunner tbr_)
void	export_reconstruction_as_ij ()
Package Attributes
JButton	exportButton
JButton	closeButton
JLabel	time_msg
Private Member Functions
GridBagConstraints	canvas_pos ()
GridBagConstraints	status_pos ()
GridBagConstraints	time_pos ()
GridBagConstraints	buttons_pos ()
GridBagConstraints	pixel_size_pos ()
GridBagConstraints	blur_pos ()
void	set_status (String s)
void	set_time (String s)
synchronized void	update_canvas ()
synchronized FloatProcessor	reconstruct ()
Private Attributes
ImagePlus	linear_reconstruction
ImageCanvas	canvas
JButton	stopButton
Color	exportButtonColor
JLabel	status
FloatSliderWithBox	blur_fwhm
FloatSliderWithBox	reconstructed_pixel_size
Panel	complete
JPanel	buttons
ThreeBRunner	tbr
ArrayList< Spot >	pts
Rectangle	roi
double	zoom = 0.01
double	reconstruction_blur_fwhm = .5
double	pixel_size_in_nm
String	filename
int	iterations = 0

Detailed Description

Control panel for running 3B plugin and providing interactive update.

Definition at line 888 of file three_B.java.

Constructor & Destructor Documentation

EControlPanel::EControlPanel	(	Rectangle	roi_,
		double	ps_,
		String	filename_,
		ThreeBRunner	tbr_
	)		`[inline, package]`

Definition at line 918 of file three_B.java.

References FloatSliderWithBox::addChangeListener(), blur_fwhm, blur_pos(), buttons, buttons_pos(), canvas, canvas_pos(), closeButton, complete, exportButton, exportButtonColor, filename, linear_reconstruction, pixel_size_in_nm, pixel_size_pos(), pts, reconstruct(), reconstructed_pixel_size, ThreeBRunner::register(), roi, set_status(), set_time(), FloatSliderWithBox::setFormat(), FloatSliderWithBox::setUnits(), status, status_pos(), stopButton, tbr, time_msg, and time_pos().

    {
        //Constract superclass
        super(filename_);

        tbr = tbr_;
        filename=filename_;

        roi = roi_;
        pixel_size_in_nm = ps_;
        pts = new ArrayList<Spot>();

    
        //Now generate the dialog box
        complete = new Panel(new GridBagLayout());

        //Create the image viewer
        linear_reconstruction = new ImagePlus();
        linear_reconstruction.setProcessor(reconstruct());
        canvas = new ImageCanvas(linear_reconstruction);
        
        //Make the image scrollable. This seems to work, if the correct cargo-culting
        //is performed with the gridbaglayout fill constraints. I don't really understand why.
        ScrollPane scroll = new ScrollPane();
        scroll.add(canvas);
        complete.add(scroll, canvas_pos());

        //Create the status message
        status = new JLabel();
        if(tbr != null)
            set_status("Running.");
        else
            set_status("Using loaded data.");
        complete.add(status, status_pos());
        
        //Create the ETA massage
        time_msg = new JLabel();
        if(tbr != null)
            set_time("unknown");
        else
            set_time("not running");
        complete.add(time_msg, time_pos());
        

        
        //The two control sliders
        blur_fwhm = new FloatSliderWithBox("Reconstruction blur FWHM", 0, 150, 100.0, 5, false);
        blur_fwhm.setUnits("nm").setFormat("%5.1f");
        blur_fwhm.addChangeListener(new SomethingChanges(this));
        complete.add(blur_fwhm, blur_pos());

        reconstructed_pixel_size = new FloatSliderWithBox("Reconstructed pixel size", 1, 300, 10.0, 5, true);
        reconstructed_pixel_size.setUnits("nm").setFormat("%5.1f");
        reconstructed_pixel_size.addChangeListener(new SomethingChanges(this));
        complete.add(reconstructed_pixel_size, pixel_size_pos());

        //The button bar
        buttons = new JPanel();
        
        exportButton = new JButton("Export...");
        exportButton.addActionListener(new ExportButtonListener(this));
        buttons.add(exportButton);
        exportButtonColor = exportButton.getBackground();
        
        //No point in having a stop button if this is just a viewer
        if(tbr != null)
        {
            stopButton = new JButton("Stop");
            stopButton.addActionListener(new StopButtonListener(this));
            buttons.add(stopButton);
        }

        closeButton = new JButton("Close");
        closeButton.addActionListener(new CloseButtonListener(this));
        buttons.add(closeButton);


        complete.add(buttons, buttons_pos());

        getContentPane().add(complete);
        
        //This class knows how to handle window close events.
        //Don't close the window by default, so we can try to bring up a 
        //confirmation dialog.
        addWindowListener(this);
        setDefaultCloseOperation(DO_NOTHING_ON_CLOSE);
        

        //Cargo culting...
        pack();
        setVisible(true);
        validate();


        //Start the 3B thread, if we have one to run.
        if(tbr != null)
        {
            tbr.register(this);
            Thread t = new Thread(tbr);
            t.start();
        }
    }

Member Function Documentation

GridBagConstraints EControlPanel::canvas_pos ( ) [inline, private]

Definition at line 1022 of file three_B.java.

Referenced by EControlPanel().

    {
        GridBagConstraints g = new GridBagConstraints();
        g.gridx = 0;
        g.gridy = 0;
        g.fill = GridBagConstraints.BOTH;
        g.weightx=100;
        g.weighty=100;
        return g;
    }

GridBagConstraints EControlPanel::status_pos ( ) [inline, private]

Definition at line 1033 of file three_B.java.

Referenced by EControlPanel().

    {
        GridBagConstraints g = new GridBagConstraints();
        g.gridx = 0;
        g.gridy = 1;
        g.anchor = GridBagConstraints.FIRST_LINE_START;
        g.fill = GridBagConstraints.BOTH;
        return g;
    }

GridBagConstraints EControlPanel::time_pos ( ) [inline, private]

Definition at line 1043 of file three_B.java.

Referenced by EControlPanel().

    {
        GridBagConstraints g = new GridBagConstraints();
        g.gridx = 0;
        g.gridy = 2;
        g.anchor = GridBagConstraints.FIRST_LINE_START;
        g.fill = GridBagConstraints.BOTH;
        return g;
    }

GridBagConstraints EControlPanel::buttons_pos ( ) [inline, private]

Definition at line 1052 of file three_B.java.

Referenced by EControlPanel().

    {
        GridBagConstraints g = new GridBagConstraints();
        g.gridx = 0;
        g.gridy = 5;
        g.fill = GridBagConstraints.BOTH;
        return g;
    }

GridBagConstraints EControlPanel::pixel_size_pos ( ) [inline, private]

Definition at line 1061 of file three_B.java.

Referenced by EControlPanel().

    {
        GridBagConstraints g = new GridBagConstraints();
        g.gridx = 0;
        g.gridy = 4;
        g.anchor = GridBagConstraints.FIRST_LINE_START;
        g.fill = GridBagConstraints.BOTH;
        return g;
    }

GridBagConstraints EControlPanel::blur_pos ( ) [inline, private]

Definition at line 1071 of file three_B.java.

Referenced by EControlPanel().

    {
        GridBagConstraints g = new GridBagConstraints();
        g.gridx = 0;
        g.gridy = 3;
        g.anchor = GridBagConstraints.FIRST_LINE_START;
        g.fill = GridBagConstraints.BOTH;
        return g;
    }

void EControlPanel::set_status ( String s ) [inline, private]

Definition at line 1081 of file three_B.java.

References status.

Referenced by EControlPanel(), and send_status_text_message().

    {
        status.setText("Status: " + s);
    }

void EControlPanel::set_time ( String s ) [inline, private]

Definition at line 1086 of file three_B.java.

References time_msg.

Referenced by EControlPanel(), and send_time_text_message().

    {
        time_msg.setText("Estimated time: " + s);
    }

synchronized void EControlPanel::update_canvas ( ) [inline, private]

Generic redraw function which recomputes the reconstruction.

this is a synchronized method since it makes use of the shared writable array of points.

Definition at line 1094 of file three_B.java.

References blur_fwhm, canvas, ThreeBGlobalConstants::critical_iterations, exportButton, exportButtonColor, FloatSliderWithBox::getValue(), iterations, linear_reconstruction, pixel_size_in_nm, reconstruct(), reconstructed_pixel_size, reconstruction_blur_fwhm, and zoom.

Referenced by send_update_canvas_event().

    {
        reconstruction_blur_fwhm = blur_fwhm.getValue();
        zoom = pixel_size_in_nm / reconstructed_pixel_size.getValue();

        linear_reconstruction.setProcessor(reconstruct());
        linear_reconstruction.updateImage();
        linear_reconstruction.updateAndRepaintWindow();
        canvas.repaint();   
        //Update the canvas size and viewport to prevent funny things with zooming.
        canvas.setDrawingSize(linear_reconstruction.getWidth(), linear_reconstruction.getHeight());
        canvas.setSourceRect(new Rectangle(linear_reconstruction.getWidth(), linear_reconstruction.getHeight()));
        //validate();
        //pack();

        if(iterations >= ThreeBGlobalConstants.critical_iterations)
        {
            exportButton.setBackground(exportButtonColor);
        }
        else
        {
            exportButton.setBackground(Color.RED);
        }

    }

void EControlPanel::windowOpened ( WindowEvent e ) [inline]

Definition at line 1123 of file three_B.java.

{ }

void EControlPanel::windowClosed ( WindowEvent e ) [inline]

Definition at line 1124 of file three_B.java.

{}

void EControlPanel::windowDeactivated ( WindowEvent e ) [inline]

Definition at line 1125 of file three_B.java.

{ }

void EControlPanel::windowActivated ( WindowEvent e ) [inline]

Definition at line 1126 of file three_B.java.

{ }

void EControlPanel::windowDeiconified ( WindowEvent e ) [inline]

Definition at line 1127 of file three_B.java.

{ }

void EControlPanel::windowIconified ( WindowEvent e ) [inline]

Definition at line 1128 of file three_B.java.

{ }

void EControlPanel::windowClosing ( WindowEvent e ) [inline]

Send a stop message to the thread if the window is closed.

Definition at line 1131 of file three_B.java.

References ThreeBRunner::has_stopped(), ThreeBRunner::stop_thread(), and tbr.

    {
        if(tbr != null && !tbr.has_stopped())
        {
            int confirmed = JOptionPane.showConfirmDialog(null, "3B still running! Closing will terminate the run. Really close?", "User Confirmation", JOptionPane.YES_NO_OPTION);

            if (confirmed == JOptionPane.YES_OPTION)
            {
                dispose();
                tbr.stop_thread();
            }

        }
        else
        {
            //OK to close
            dispose();
        }
    }

void EControlPanel::export_reconstruction_as_ij ( ) [inline, package]

Generate a fresh ImageJ image in a standard imageJ window, so that ti can be manipulated using the usual ImageJ commands.

The image is size calibrated, so scalebars are easy to add.

Definition at line 1154 of file three_B.java.

References filename, FloatSliderWithBox::getValue(), linear_reconstruction, and reconstructed_pixel_size.

Referenced by ExportButtonListener::actionPerformed().

    {
        ImageProcessor export = linear_reconstruction.getProcessor().duplicate();
        ImagePlus export_win = new ImagePlus(filename + " reconstruction", export);
        export_win.getCalibration().pixelWidth = reconstructed_pixel_size.getValue();
        export_win.getCalibration().pixelHeight = reconstructed_pixel_size.getValue();
        export_win.getCalibration().setXUnit("nm");
        export_win.getCalibration().setYUnit("nm");
        export_win.show();
        export_win.updateAndDraw();
    }

synchronized FloatProcessor EControlPanel::reconstruct ( ) [inline, private]

Compute a brand new reconstruction.

Definition at line 1167 of file three_B.java.

References pixel_size_in_nm, pts, reconstruction_blur_fwhm, roi, and zoom.

Referenced by EControlPanel(), and update_canvas().

    {
        //Reconstruct an image which is based around the ROI in size
        int xoff = (int)roi.x;
        int yoff = (int)roi.y;

        int xsize = (int)Math.ceil(roi.width * zoom);
        int ysize = (int)Math.ceil(roi.height * zoom);
        
        //New blank image set to zero
        FloatProcessor reconstructed = new FloatProcessor(xsize, ysize);

        for(int i=0; i < pts.size(); i++)
        {
            
            //Increment the count 
            int xc = (int)Math.floor((pts.get(i).x-xoff) * zoom + 0.5);
            int yc = (int)Math.floor((pts.get(i).y-yoff) * zoom + 0.5);
            float p = reconstructed.getPixelValue(xc, yc);
            reconstructed.putPixelValue(xc, yc, p+1);
        }

        double blur_sigma = reconstruction_blur_fwhm / (2 * Math.sqrt(2 * Math.log(2))) * zoom / pixel_size_in_nm;

        (new GaussianBlur()).blurGaussian(reconstructed, blur_sigma, blur_sigma, 0.005);
        return reconstructed;
    }

void EControlPanel::issue_stop ( ) [inline]

Definition at line 1196 of file three_B.java.

References ThreeBRunner::stop_thread(), stopButton, and tbr.

Referenced by StopButtonListener::actionPerformed().

    {
        if(tbr != null)
            tbr.stop_thread();
        stopButton.setEnabled(false);
    }

synchronized void EControlPanel::append	(	final ArrayList< Spot >	p,
		int	its
	)		`[inline]`

Callback issued by the runnre thread which appends the latest set of points to the array.

This is synchronized since it involves the shared writable array of points.

Definition at line 1208 of file three_B.java.

References iterations, and pts.

Referenced by ThreeBLoader::run(), and ThreeBRunner::send_new_points().

    {
        for(int i=0; i < p.size(); i++)
            pts.add(p.get(i));

        iterations = its;
    }

void EControlPanel::send_update_canvas_event ( ) [inline]

Callback for causing a recomputation of the reconstruction.

This is a safe method for telling the class to recompute and redraw the reconstruction. It can be called from anywhere, but ensures that the redraw happens in the GUI thread.

Definition at line 1220 of file three_B.java.

References update_canvas().

Referenced by ThreeBLoader::run(), ThreeBRunner::send_new_points(), and SomethingChanges::stateChanged().

    {
        SwingUtilities.invokeLater(
            new Runnable() {
                final public void run() {
                        update_canvas();
                    }
                }
        );
    }

void EControlPanel::die ( final String s ) [inline]

Callback which causes a fatal termination of the 3B control panel.

This is generally caused by something changing such that the error condition was not seen in the Java code, but was seen in C++. Ought never to be called.

Definition at line 1235 of file three_B.java.

Referenced by ThreeBRunner::die().

    {
        SwingUtilities.invokeLater(
            new Runnable() {
                final public void run() {
                        ij.IJ.showStatus("3B run terminated due to an error.\n");
                        JOptionPane.showMessageDialog(null, "Error: "+s, "Fatal error", JOptionPane.ERROR_MESSAGE);
                        dispose();
                    }
                }
        );
    }

void EControlPanel::send_status_text_message ( final String s ) [inline]

Callback to update the status message safely.

Definition at line 1249 of file three_B.java.

References set_status().

Referenced by ThreeBLoader::run(), ThreeBRunner::run(), and ThreeBRunner::send_message_string().

    {
        SwingUtilities.invokeLater(
            new Runnable(){
                final public void run() {
                        set_status(s);
                    }
                }
        );
    }

void EControlPanel::send_time_text_message ( final String s ) [inline]

Callback to update the status message safely.

Definition at line 1262 of file three_B.java.

References set_time().

Referenced by ThreeBRunner::send_new_points().

    {
        SwingUtilities.invokeLater(
            new Runnable(){
                final public void run() {
                        set_time(s);
                    }
                }
        );
    }