ThreeBLoader Class Reference

Plugin class to load up an old 3B run. More...

List of all members.

Public Member Functions
void	run (String arg)
Private Member Functions
void	close (InputStream i)

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Detailed Description

Plugin class to load up an old 3B run.

Definition at line 27 of file ThreeBLoader.java.

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Member Function Documentation

void ThreeBLoader::close

(

InputStream

i

)

[inline, private]

Definition at line 29 of file ThreeBLoader.java.

Referenced by run().

    {
        //Not sure what to do here...
        if(i != null)
        {
            try{
                i.close();
            }
            catch(IOException ioe)
            {
                Toolkit.getDefaultToolkit().beep();
                ij.IJ.showStatus("Error closing file: " + ioe.getMessage());
            }
        }
    }

void ThreeBLoader::run

(

String

arg

)

[inline]

Definition at line 45 of file ThreeBLoader.java.

References EControlPanel::append(), close(), EControlPanel::send_status_text_message(), EControlPanel::send_update_canvas_event(), Spot::x, and Spot::y.

                                {
        InputStream in = null;
        String name;
        double ps;

        try{
            if(arg.equals("test"))
            {
                name = "test_data.txt";

                try{
                    in = new GZIPInputStream(getClass().getClassLoader().getResourceAsStream("test_data.txt.gz"));
                }
                catch(IOException ioe)
                {
                    Toolkit.getDefaultToolkit().beep();
                    ij.IJ.showStatus("Could not open test data: " + ioe.getMessage());
                    return;
                }
                ps=100;
            }
            else
            {
                OpenDialog o = new OpenDialog("Open 3B run...", null);
                name = o.getFileName();
                
                try{
                    in = new FileInputStream(o.getDirectory() + o.getFileName());
                }
                catch(java.io.FileNotFoundException ferr)
                {
                    Toolkit.getDefaultToolkit().beep();
                    ij.IJ.showStatus("Error opening file: " + ferr.getMessage());
                    return;
                }



                GenericDialog g = new GenericDialog("Pixel size");
                g.addNumericField("Pixel size", 100., 0, 5, "nm");
                g.showDialog();
                ps = g.getNextNumber();
            }

            //Yay @ cargoculting
            InputStreamReader d = new InputStreamReader(in);
            BufferedReader r = new BufferedReader(d);

            String line;
            final ArrayList<Spot> spots = new ArrayList<Spot>();
            int iterations=0;
            Rectangle roi=null;
            final double pixel_size_in_nm_ = ps;

            while((line = r.readLine()) != null)
            {
                String tokens[] = line.split("\\p{Space}+");

                if(tokens[0].equals("PIXELS"))
                {
                    if((tokens.length - 1)%2 != 0)
                        throw new IOException("corrupt file (bad pixels line)");

                    for(int i=1; i < tokens.length; i+= 2)
                    {
                        int x, y;
                        try
                        {
                            x = Integer.parseInt(tokens[i+0]);
                            y = Integer.parseInt(tokens[i+1]);
                        }
                        catch(NumberFormatException nerr)
                        {
                            throw new IOException("corrupt file (bad pixel coordinate)");
                        }

                        if(roi == null)
                            roi = new Rectangle(x, y, 1, 1);
                        else
                            roi.add(x, y);
                    }
                }

                if(tokens[0].matches("PASS[0-9]+:"))
                {
                    iterations++;

                    if((tokens.length - 1)%4 != 0)
                        throw new IOException("corrupt file (pad pass line)");

                    for(int i=1; i < tokens.length; i+= 4)
                    {
                        Spot s = new Spot();
                        try
                        {
                            s.x = Double.parseDouble(tokens[i+2]);
                            s.y = Double.parseDouble(tokens[i+3]);
                        }
                        catch(NumberFormatException nerr)
                        {
                            throw new IOException("corrupt file (bad spot position)");
                        }

                        spots.add(s);
                    }
                }

            }
            if(roi == null)
                throw new IOException("corrupt file (no ROI)");

            final String fname = name;
            final Rectangle roi_ = roi;
            final int its = iterations;
            SwingUtilities.invokeLater(
            new Runnable() {
                    public void run() {
                            EControlPanel e = new EControlPanel(roi_, pixel_size_in_nm_, fname, null);
                            e.append(spots, its);
                            e.send_update_canvas_event();
                            e.send_status_text_message("Using " + fname + ": " + Integer.toString(its) + " iterations.");
                    }
            }
            );




        }
        catch(IOException another_ioe){
            Toolkit.getDefaultToolkit().beep();
            ij.IJ.showStatus("Error reading data: " + another_ioe.getMessage());
        }
        finally{
            close(in);
        }

    }

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The documentation for this class was generated from the following file:

• ThreeBLoader.java